Shopify Business Central can sync online orders, inventory, etc. The free Microsoft app, though, reveals glaring weaknesses for most. Shopify order synchronization problems, tax discrepancies, and performance are problems that users then encounter. This blog reveals those issues and recommends more optimal means of handling a Dynamics 365 Business Central Shopify connection. 

According to the Microsoft Dynamics Community post “Shopify connector,” the free Shopify Business Central connector shows an “End of support” date of March 1, 2024—updates after that often break syncing entirely and force a full reinstall to restore functionality. 

What is the Free Shopify Connector for Dynamics 365 Business Central? 

It’s a no-cost integration released by Microsoft that links Shopify with Dynamics 365 BC—but lacks core features like returns, variants, and real-time taxes. 

Read more in Microsoft Docs: Getting started with the connector for Shopify. 

What Are The Common Connector Limitations? 

For a full list of known issues, see Microsoft’s Shopify Connector Troubleshooting Guide. 

One merchant reported on the Khaos Control Cloud support portal that imported Shopify orders frequently showed incorrect VAT amounts—necessitating manual corrections for dozens of transactions. 

Discrepancy in Order Value: Individuals will be noticing unusual tax or shipping amounts in Business Central. Manual corrections, which slow down your processes. 

Lack of Advanced Variant Product Support: Variant listings are driving your store. The free ERP integration from Shopify may bypass appropriate mapping for size or colour combinations. 

Integration Gap for Return & Refund: Most sellers process returns. The free connector does not map item replacements or partial refunds very well. 

Inaccurate Tax Calculation: Others notice unexpected tax or duty amounts. You may be presented with repeated order adjustments. 

Multi-Currency Weakness: Shopify multi-currency issues are problematic. Euro or CAD orders may not be correctly reflected in Business Central. 

Lack of In-Store Pickup Handling: Local pick-up merchants have those orders reflect as shipped. That confuses and hinders actual tracking. 

Multilingual Product Problems: You may need different descriptions in different regions. The free connector does not have Shopify multi-language product description sync. 

According to Gartner, the digital commerce platform market grew by 11.5% in 2023 to $8.9 billion and is forecast to keep climbing through 2024–25. By 2030, B2B ecommerce will center on customer-centricity, connectivity, agility, and intelligence. 

Key Takeaway: The free connector lacks essentials—variant support, refund mapping, and real-time tax sync—forcing manual fixes and slowing you down. 

What Are The Additional Drawbacks That Impede Growth? 

Processing & Numerosity 

Large sellers would prefer to filter orders by shipping method or region. Free app lacks extensive order filtering. Shopify synchronization speed is too slow, allowing sold-out products to be repurchased. 

Constant Reorganization 

Shopify or Business Central updates frequently disrupt free integration. You might need to reinstall or perform repeated setups. 

Manual Fixes Add Up 

If shipping or returns are not syncing in a system, employees have to correct data in ERP. That takes time and increases risk. 

How APPSeCONNECT can Assist? 

Your B2B business can be leveraging APPSeCONNECT to have more accurate real-time data synchronization. Our solution accommodates Shopify Business Central synchronization of taxes, refunds, variants, and multi-store configurations.  

You will be automating complex scenarios such as how to resolve Shopify order value mismatch in Business Central without commonplace repetitive manual patches. We also take care of multi-currency expansions and quicker synchronization. That means fewer errors, saved time, and satisfied customers. 

APPSeCONNECT also ensures data consistency with role-based ERP access and compliance with enterprise security standards. 

Third-party tools like Celigo and Patchworks offer basic BC–Shopify syncing, but lack APPSeCONNECT’s pre-built Business Central templates, enterprise-grade error handling, AI-driven auto-mapping, and full compliance with GDPR, CCPA/CPRA, PCI DSS, and MHRA. 

Our solution automates complex scenarios—like resolving Shopify order-value mismatches in BC—without repetitive manual patches. You’ll also get: 

CCPA/CPRA Compliance: Built-in data-handling rules to meet U.S. privacy requirements. 

UK GDPR (Post-Brexit) Controls: Automatic cross-border data protections plus VAT logic for seamless EU–UK fulfillment. 

Enterprise-Grade Security: Role-based ERP access, PCI DSS encryption, and SOC 2/ISO 27001 certifications. 

Real-World Impact

• In our NaturesPlus Case Study, APPSeCONNECT reduced BC order-sync errors by 78% and cut manual reconciliation time by 65%. 
• With BellyGood Case Study, variant syncing issues were eliminated, boosting fulfillment speed by 40%. 

These results translate into fewer stockouts, faster order turnaround, and happier customers. 

Free Connector vs. APPSeCONNECT 

• Supports variants 
• Handles returns/refunds 
• Fast sync speed 
• Real-time tax mapping 

Key Takeaway: Automate BC–Shopify workflows with built-in compliance (CCPA/CPRA, UK GDPR), AI-driven error healing, and real-time sync to eliminate hours of manual work. 

See how APPSeCONNECT helped NaturesPlus scale their BC integration. 

Top 10 Limitations of the Free Connector 

1. Order value mismatches (tax/shipping amounts often import incorrectly)
2. Variant sync gaps (size, color or custom options don’t map)
3. Refund and return mapping issues (partial refunds or replacements fail to sync)
4. Inaccurate tax calculations (unexpected adjustments, VAT/duty errors)
5. Multi-currency shortcomings (non-USD orders aren’t reflected properly)
6. No in-store pickup support (local-pickup orders show as shipped)
7. Multilingual product descriptions aren’t synced
8. Limited order filtering (can’t segment by channel, region, or shipping method)
9. Frequent breakages on Business Central or Shopify updates (requires reinstall)
10. Slow sync performance (lags lead to oversells and stockouts) 

Conclusion 

Free Shopify Business Central connector may sound appealing but comes with severe syncing flaws. You will struggle with missing features, tax errors, and variant limitations. For seamless Dynamics 365 Business Central Shopify integration, then, use something more holistic such as APPSeCONNECT. Ready to avoid manual corrections? Book a demo and unlock actual integration success. 

Sync orders right the first time. Get a personalized connector walkthrough.