When your orders fall through the cracks, your inventory data feels unreliable, and finance is stuck in spreadsheet limbo, something is clearly broken. You may have tried patching things up between Shopify and Business Central before. But without a disciplined, tested approach, even the best intentions create more chaos.
This guide helps you take the guesswork out of integration. We show you exactly what syncs, what path to follow, and how to avoid the mistakes that cause most projects to unravel.

 

Connecting Shopify with Microsoft Business Central is beyond an IT integration; it is the way your storefront and back office functions on a common point of truth. With proper setups in place, orders are automatically posted, inventory is up to date, and the finance department finishes its closing quicker, and no longer has to rely on manual spreadsheets to update the customer. 

This guide helps you understand what you can expect when taking a disciplined approach to roll out: which data synchronizes, what path you should select to integrate, how to introduce in controlled incremental stages, and what you can do to ensure that your solution remains reliable as you scale. You will understand when the native connector will work and when it should be replaced with custom development, and when orchestration and monitoring capabilities in an iPaaS are worth the additional cost. 

If you’ve been burned by brittle bridges before, you’ll learn the guardrails that prevent déjà vu. Use this as your working checklist for Shopify ERP integration that sticks.

What Integrates Between Shopify and Business Central

You’re syncing the “truth” across both systems so they always show the same reality. At a high level, five things move in lockstep: products & variants, inventory & locations, customers & pricing, orders, payments & taxes, and fulfillments, returns & refunds. 

Nail these mappings once, and everything downstream, picking, posting, payouts, and customer updates, stays clean without manual fixes.

1. Products & Variants

You’re aligning merchandising in Shopify with item records in BC, so product identity is consistent everywhere.

What to Map

• Map each Shopify SKU to a single Business Central Item No. Use one variant per SKU and keep SKUs unique across the entire catalog.
• Sync titles, options, and attributes from Shopify to the matching Item fields and variant dimensions in Business Central.
• Copy descriptions, images, and tags/collections to the appropriate Item details and media fields in Business Central.
• If you sell bundles or kits, pick one model: manage them in a Shopify bundle app or model them as a kit/BOM in Business Central. Don’t try to maintain both.

Common Mistakes 

• Renaming SKUs during cutover breaks the SKU–Item link and can create duplicates. Freeze SKU changes until after go-live.
• Letting both systems edit the product master causes conflicts and data drift. Assign a single product master (Shopify or BC) and enforce it.

1. Inventory & Locations

You’re keeping “what’s available” aligned across warehouses, stores, and the site.

What to Map

• Map each Shopify location to a unique Business Central Location Code so stock movements are recorded consistently.
• Sync available-to-sell quantities with Business Central projected availability, factoring in reservations and allocations to avoid phantom stock.
• Set safety stock, backorder rules, and buffer quantities for each location to prevent overselling and protect service levels.

Pro Tips 

• Push fast-movers near real time; batch slow-movers on a schedule.
• Run nightly reconciliation to catch drift early

1. Customers & Pricing

You’re matching shoppers and accounts to customers and price logic in BC.

What to Map 

• Map Shopify customers and companies to the corresponding Business Central customer records and customer price groups.
• Synchronize tax flags, exemptions, and addresses, exposing only the minimum PII required in each system.
• For B2B accounts, carry over contract price lists, payment terms, purchase order numbers, and credit limits so sales orders apply the correct negotiated conditions automatically.

Guardrails

• Choose a single price authority, either Business Central or Shopify, and stick to it.
• Mirror only the fields that support, finance, and operations need; leave everything else where it belongs.

1. Orders, Payments & Taxes

You’re turning carts into auditable sales docs with the right accounting treatment.

What to Map

• Map Shopify orders to Business Central Sales Orders (or directly to Sales Invoices if your workflow requires it).
• Record payment-gateway transactions and payouts as cash entries in Business Central and reconcile them during bank reconciliation.
• Use a single tax engine, either Shopify or Business Central, and ensure identical rounding rules and jurisdiction settings to avoid discrepancies.

Implementation Risks

• If your workflow includes split shipments, configure Business Central to support partial picks and multiple fulfillments; otherwise, orders will stall or mispost.
• Map discounts, gift cards, and store-credit transactions to explicit GL accounts so postings remain auditable and the month-end close stays clean.

1. Fulfillments, Returns & Refunds

You’re closing the loop so customers see tracking and finance sees clean reversals.

What to Map

• After a shipment is posted in Business Central, push the carrier and tracking number back to the corresponding Shopify fulfillment so customers receive accurate updates.
• For returns, translate the RMA into a Credit Memo in Business Central and process the refund back to the original payment method to preserve a clean audit trail.
• Standardize return reasons and map each one to an analysis code in Business Central so you can report on trends and identify root causes.

Golden Rule

• If finance can’t audit it, don’t automate it yet. Add the missing field, then automate.

Choose Your Integration Approach

1. Native BC–Shopify Connector

Use the standard connector when you want speed to value and opinionated, proven mappings without heavy code.

When it fits

• You run a single Shopify store and one (or a small number of) Business Central companies.
• Your catalog uses standard variants and does not depend on complex bundles or kits.
• Your pricing and tax rules are straightforward and don’t require custom logic.
• Your team prefers configuration over custom development and long-term code maintenance.

What you gain

• You finish the build faster and carry less maintenance overhead.
• You inherit mappings that follow Microsoft and Shopify best practices, which reduces rework and surprises later.

1. Custom API Integration

Go custom when you need full control over data shapes, timing, and business rules.

When it fits

• You sell complex bundles or build-to-order products, or you require special fulfillment logic such as split manufacturing and drop-ship hybrids.
• You support heavy B2B flows, including quotes-to-orders, contract pricing, and hierarchical accounts with delegated purchasing.
• You operate multiple brands, multiple stores, or multiple Business Central companies that share catalogs but need distinct rules and presentation.
• You must orchestrate tightly with a WMS or 3PL and meet strict compliance or audit requirements.

What you gain 

• You get exact behavior aligned to your processes, not approximations.
• You implement tailored error handling and observability that your team can trust.
• You establish future-proof integration patterns that extend cleanly to new channels and systems.

1.  iPaaS / Middleware

Choose middleware when you orchestrate many systems and want monitoring, retries, and audit trails out of the box.

When it fits

• You’re coordinating Shopify, BC, WMS, CRM, marketplaces, 3PLs
• Your team prefers visual flows and admin over code
• You want alerting and dashboards on day one

Trade-offs

• You’ll incur a recurring subscription cost and be responsible for operating one additional integration hub.
• You can ship changes faster and monitor flows more easily, though you’ll also be tied to the middleware vendor’s roadmap and uptime.

Call it Shopify integration with ERP or unified commerce, the right choice is the one that keeps data correct with the least ops overhead.

How All Your Ducks Help

We at All Your Ducks turn an integration project into a clear plan, a durable build, and a calm handoff that your team can trust.

Here’s how we support you from kickoff to scale without the chaos.

What We Do

• We run a Success Criteria Workshop to lock masters, define success metrics, and finalize field mappings before any data moves.
• We build the integration with the native connector, custom APIs, or an iPaaS, whichever best fits your complexity, budget, and timeline.
• We manage UAT and cutover with golden test cases, a documented rollback plan, and hands-on hypercare, so go-live is boring (in the best way).
• We provide ongoing support with monitoring dashboards, nightly reconciliation jobs, audit assistance, and scale work as your volume and channels grow.

If you’re ready to replace “connect the systems” with “it just works,” we’ll map it, build it, and make it stick.

Bottom Line

Choose the integration pattern, native connector, custom API, or iPaaS, based on complexity and governance. Set single sources of truth for product, price, inventory, tax, and customer data; document mappings, and include only required fields. Validate with repeatable UAT and freeze SKUs before cutover. After go-live, enforce idempotent order posting, bounded retries, monitored dead-letter queues, and nightly reconciliation. 

Use one tax engine and explicit GL paths for discounts, payouts, and refunds. Sync projected availability (including reservations) and maintain cycle counts. Assign owners for alerts, dashboards, and exception clearance. Executed this way, Shopify ERP integration is reliable and scalable; executed loosely, shopify integration with ERP invites rework and risk.

Book a 45-minute integration diagnostic with All Your Ducks.

Ready to move?

FAQs

1. What is ERP integration with Shopify?

It’s the real-time connection between your Shopify store and an ERP, so both share one source of truth. Products, inventory, customers, orders, taxes, shipments, returns, and refunds stay in sync. Manual entry drops. Stock accuracy and financial postings improve. In short, Shopify ERP integration replaces spreadsheets with controlled, auditable flows.

2. Which ERP systems integrate with Shopify?

Most leading ERPs do. Microsoft Dynamics 365 Business Central integrates via a native connector. Oracle NetSuite, SAP Business One and S/4HANA, Acumatica, Sage (Intacct, X3), and Infor CloudSuite connect through certified connectors, iPaaS platforms, or custom APIs. Depth varies by approach, so match the method to your catalog, B2B needs, and compliance requirements.

3. Do I need an ERP with Shopify?

Not always. If you have a small catalog, one location, simple pricing and tax, and basic accounting, Shopify alone can work. Add an ERP when complexity rises: multiple warehouses or companies, large SKU counts, B2B price lists and terms, MRP or purchase-to-pay, audit demands, or slow, error-prone closes. When stock accuracy, postings, or reporting start slipping, Shopify integration with ERP usually pays for itself.

4. How do I integrate Shopify with an ERP?

Pick an approach, native connector for speed, iPaaS for orchestration and monitoring, or custom APIs for full control. Define system-of-record rules for product, price, inventory, tax, and customer data. Map fields and GL paths. Build and test in a sandbox with “golden” SKUs and orders. Enforce idempotent order posting, bounded retries, and a dead-letter queue. Cut over with UAT passed twice, SKUs frozen, and nightly reconciliation for orders, inventory, and cash. Maintain dashboards and human-routed alerts. Done well, your shopify ERP integration is predictable, auditable, and scalable.

Introduction: Start with the Pain
Manual entries. Inventory mismatches. Orders slipping through the cracks. If your storefront and ERP feel like two different worlds, you’re likely wasting hours and losing revenue. Most growing ecommerce businesses hit a wall when their backend systems can’t keep up with the front-end pace. That’s where integration makes all the difference.

Let’s show you how to get all your ducks in a row by syncing your Shopify (or other) storefront with Microsoft Dynamics 365 for faster, cleaner operations—without the chaos.

 

What eCommerce Integration with Dynamics 365 Actually Means

When your storefront and ERP talk in real-time, you eliminate silos. Products, orders, inventory, tax, and customer data flow as one, not as a patchwork of spreadsheets and error-prone processes.

 

1. Core Data Domains That Must Be Synced

Product & Pricing:

• Pick a single system of truth—don’t let both sides manage the catalog.
• Keep SKUs stable to avoid link breaks during cutover.
• Ensure all images, tags, attributes, and pricing stay aligned.

Inventory & Availability:

• Avoid overselling by syncing real-time availability including reservations.
• Match Shopify locations with Dynamics location codes.

Customers & Accounts:

• Merge customer profiles so support and sales see the full picture.
• Stick to just the necessary fields to minimize risk.

Orders, Payments & Tax:

• Post orders as Sales Orders or Invoices per your process.
• Align payment capture with revenue recognition policy.
• Use a single tax engine to avoid rounding issues.

Fulfillments, Returns, & Refunds:

• Push tracking info back to the store automatically.
• Post refunds to the original payment method with a clean audit trail.

 

2. Choose the Right Architecture: Native, iPaaS, or Custom

Native Connector:
Ideal for businesses running one or a few stores with straightforward needs. Fastest to implement, lowest overhead.

iPaaS:
Great for orchestrating multiple systems (WMS, 3PL, CRM). Visual dashboards, built-in monitoring, and faster iteration.

Custom API:
Perfect when you need total control—complex catalogs, multi-brand support, or strict B2B requirements.

 

3. Finance & Ops: Where Integration Hits the P&L

• Order-to-cash flows must be tight to speed up the close.
• Inventory sync protects margins and service levels.
• Tax accuracy avoids audit pain later.

 

4. CRM Integration: Why It’s Not Just a Nice-to-Have

When sales, marketing, and service teams see ecommerce data in Dynamics 365 CRM, every interaction improves. Orders, preferences, warranties—all in one place.

 

5. 4-Phase Implementation Path That Reduces Risk

1. Discovery: Lock system-of-records and field mappings before any code.
2. Build: Start in a sandbox. Add idempotency and retries from the start.
3. UAT: Golden test cases prove the flow. Finance signs off.
4. Cutover: Go live with rollback in hand. Hypercare keeps it calm.

 

Why Partner with All Your Ducks

We’ve seen too many brands try to “just connect the systems” and end up swimming upstream. We map the integration, build it to scale, and deliver it with rigor. From UAT to go-live, we help your ducks stay in a row—and stay there.

 

Final Word: Durable, Not Delicate

Done right, Dynamics 365 ecommerce integration becomes a business capability—not a brittle project you dread revisiting.

Need to stop the post-it note chaos and start scaling?
Book a 45-minute diagnostic with All Your Ducks today.

If you are a business that sells, omni-channel selling through a unified commerce experience is crucial for growth and scalability. A pivotal strategy in getting there is through the integration of your eCommerce platform with your Enterprise Resource Planning (ERP) system. This unified commerce approach not only streamlines internal processes but also provides a seamless and personalized experience for customers.​

Understanding ERP and eCommerce Integration

At its core, ERP and eCommerce integration involves the seamless connection between a company's online storefront and its back-end ERP system. This integration facilitates the automatic exchange of data, ensuring that information such as orders, inventory levels, customer details, and financials are consistently updated across both platforms. By eliminating the need for manual data entry, businesses can reduce errors, save time, and enhance overall efficiency.​

Key Benefits of a Unified Commerce Experience

1. Enhanced Customer Satisfaction

Integrating ERP with eCommerce platforms enables businesses to provide real-time updates on product availability, order status, and shipping information. This transparency fosters trust and enhances the overall customer experience, leading to increased loyalty and repeat business.

2. Improved Inventory Management

Real-time synchronization between eCommerce and ERP systems ensures accurate inventory tracking. Businesses can avoid overselling or stockouts, leading to better inventory control and optimized stock levels.

3. Streamlined Order Processing

Automated data flow between systems accelerates order fulfillment processes. Orders placed online are immediately reflected in the ERP system, reducing processing times and minimizing the risk of errors associated with manual data entry.

4. Accurate Financial Reporting

An integrated system consolidates financial data, facilitating the generation of comprehensive reports such as trial balances, cash flow statements, and profit and loss accounts. This accuracy supports informed decision-making and financial planning.

5. Operational Efficiency

By automating routine tasks and reducing redundancy, integration allows employees to focus on strategic initiatives. This boost in productivity can lead to cost savings and a more agile business operation.

6. Scalability

As businesses grow, an integrated system can effortlessly handle increased transactions, product lines, and customer data, supporting expansion without necessitating a proportional increase in resources.

7. Enhanced Data Accuracy

With a unified system, data consistency is maintained across all departments. This accuracy is crucial for reliable reporting, forecasting, and strategic planning.

8. Regulatory Compliance

Integrated systems can assist in adhering to industry regulations by providing accurate records and facilitating compliance-related reporting. This feature is particularly beneficial in sectors with stringent regulatory requirements.

Challenges and Considerations

While the benefits are substantial, integrating eCommerce with ERP systems presents certain challenges:​

• Complexity: The integration process can be intricate, requiring careful planning and execution to ensure seamless operation.​
• Cost: Initial investment in integration can be significant, encompassing software, hardware, and implementation expenses.​
• Customization: Tailoring the integration to meet specific business needs may require additional resources and expertise.​
• Data Security: Ensuring the security of data during and after integration is paramount to protect against breaches and maintain customer trust.​

Best Practices for Successful Integration

To navigate these challenges effectively, businesses should consider the following best practices:

1. Comprehensive Planning: Define clear objectives, timelines, and resource allocations before initiating the integration process.​
2. Stakeholder Involvement: Engage key stakeholders from various departments to gather insights and ensure the integrated system meets diverse needs.​
3. Choose the Right Technology Partner: Select an experienced provider with a proven track record in ERP and eCommerce integration to guide the process.​
4. Data Mapping and Cleaning: Ensure that data from both systems are accurately mapped and cleansed to prevent inconsistencies.​
5. Robust Testing: Conduct thorough testing to identify and resolve issues before going live, ensuring the system operates as intended.​
6. Ongoing Support and Maintenance: Establish a plan for continuous monitoring and maintenance to address any future challenges promptly.​

The Right Choice

There are a number of platforms to work with for both eCommerce and ERP solutions. At All Your Ducks, we recommend Shopify as your eCommerce Platform and Microsoft Dynamics 365 Business Central as your ERP. Both tools are backed by best-in-class security and reliability, and the integration between them is one of the most powerful connections on the market. Shopify and Business Central work together to create a unified commerce experience for your customers, insuring accurate inventory, dynamic pricing, and unparalleled personalization.

Get All Your eCommerce Ducks in a Row

Integrating eCommerce platforms with ERP systems is a strategic move that can significantly enhance business operations and customer satisfaction. By creating a unified commerce experience, companies can achieve greater efficiency, accuracy, and scalability. While the integration process may involve challenges, the long-term benefits far outweigh the initial investment, positioning businesses for sustained growth in the competitive digital marketplace. At All Your Ducks, we work with businesses of all sizes to create a unified commerce experience. Contact us today to see how we can help your business grow!

 

As Microsoft prepares to roll out the 2025 Release Wave 1 for Dynamics 365 Business Central, businesses must stay informed about the upcoming changes. This release introduces several new features, mandatory updates, and deprecations that could significantly impact existing customizations and pricing structures. Understanding these changes is crucial to ensure seamless operations and to leverage the new capabilities effectively.

Key Features and Enhancements

The 2025 Release Wave 1 brings a host of new functionalities aimed at enhancing user experience and operational efficiency. While you can dig through the full list of changes here, notable updates include:​

• Copilot and AI Integration: Building upon previous AI capabilities, this release introduces features like marketing text suggestions, aiming to boost productivity across various small and medium-sized business roles. ​
• Field Service Integration: Enhanced integration with Dynamics 365 Field Service allows for better synchronization and management of service operations, providing actionable insights for schedulers and frontline workers. ​
• Application Improvements: Updates such as improved troubleshooting options for cost adjustments and extended item availability views in Field Service work orders are set to streamline operations. ​

Mandatory Updates and Deprecations

With this release, certain features that were previously optional are becoming mandatory, and some legacy functionalities are being deprecated. Key changes include:​

• Extending G/L Entry Aggregations When Posting Invoices: This feature, generally available since Update 23.1, becomes mandatory in Update 26.0 (2025 Release Wave 1). It replaces the legacy "Invoice Post. Buffer" table, addressing extensibility issues and allowing for customized implementations of G/L invoice posting. ​
• New Extensible Exchange Rate Adjustment: Introduced in Update 23.0, this feature becomes mandatory in Update 26.0. It replaces the legacy Exchange Rates Adjustment Report, offering increased extensibility, better compliance with local and industry-specific requirements, and enhanced control over exchange rate adjustments, including a posting preview and improved reporting. ​

• Transition to the New Sales Pricing Experience: One of the significant changes in this release is the transition to a new sales pricing experience. This update offers enhanced flexibility and functionality in managing sales prices. However, businesses with custom pricing tables or integrations should be aware that these customizations may require remediation to align with the new pricing structure. It's advisable to review and, if necessary, adjust custom pricing solutions to ensure compatibility with the updated system.​

• Legacy Reports Deprecation: Many legacy reports in Business Central are being deprecated due to their complexity and the technical skills required for modification. These reports are scheduled for complete removal in the 2026 Release Wave 1.

Impact on Customizations

The mandatory adoption of new features and the deprecation of legacy functionalities necessitate a thorough review of existing customizations. Businesses should:​

• Assess Current Customizations: Identify customizations that interact with deprecated features or utilize legacy tables and reports.​
• Plan for Remediation: Develop a strategy to update or replace customizations to align with the new standard functionalities. This may involve re-implementing certain processes or adopting new extensions.​
• Test Extensively: Before deploying updates to the production environment, conduct comprehensive testing to ensure that all customizations function as intended with the new release.​

Recommendations for a Smooth Transition for the 365 Business Central 2025 Release

To navigate the changes introduced in the 2025 Release Wave 1 effectively, businesses with existing customizations should consider the following steps:

• Review Customizations: Conduct a thorough audit of all custom features, including pricing tables, reports, and integrations, to identify dependencies on deprecated or modified functionalities.​
• Test Compatibility: Utilize sandbox environments to test customizations against the updated system, identifying potential conflicts or issues that may arise post-upgrade.​
• Plan Remediation: Develop a remediation plan that includes updating or replacing deprecated features, adjusting custom code to align with new functionalities, and ensuring that mandatory features are appropriately configured.​
• Stay Informed: Regularly consult Microsoft's official release notes and documentation to stay abreast of upcoming changes and best practices for implementing them.​

By proactively addressing these updates and understanding their implications, businesses can maintain operational continuity and position themselves to take full advantage of the enhancements introduced in Dynamics 365 Business Central 2025 Release Wave 1. Our team at All Your Ducks are up to speed on these and all the changes coming in Wave 1. Contact us today to make sure your business stays up and running through the update and beyond.