Introduction
In 2025, many Shopify sellers use Amazon’s FBA network to fulfill orders. It’s fast, scalable—and dangerous if not managed correctly.
Proven Tip:
Use Amazon MCF (Multi-Channel Fulfillment) through a direct integration and separate SKUs in your accounting system. This avoids duplicate inventory issues and keeps your tax records clean.
Proven Tip: Sync Shopify with Amazon MCF the Right Way
When Shopify orders are fulfilled via Amazon, you must:
- Set up Amazon MCF integration using official apps or third-party connectors like Bytestand or Connectr
- Separate FBA SKUs from Shopify-only SKUs
- Track inventory and fulfillment fees by channel
- Record FBA fees in your books monthly
- Adjust for lost, damaged, or returned items in Amazon’s system
Failure to reconcile Amazon fulfillment activity in your Shopify books can lead to COGS mismatches and audit triggers.
IRC Tax Code Relevance
Selling through both Shopify and Amazon FBA means you must track:
- Inventory properly (IRC §471)
- Fulfillment fees and shipping as deductible business expenses (IRC §162)
- Platform reporting and cross-channel revenue under proper methods (IRC §446)
- Gross receipts vs. fees under Form 1099-K (IRC §6050W)
Amazon and Shopify may both issue Form 1099-K, so double counting can occur without clean books.
Relevant IRS Forms
| Form | Purpose |
|---|---|
| Form 1125-A | Report COGS (for Amazon and Shopify inventory) |
| Form 1099-K | Issued by Amazon and/or Shopify for gross sales |
| Schedule C / Form 1065 / 1120-S | Business income reporting from both platforms |
| Form 4562 | Deduct or depreciate fulfillment-related equipment or software |
| Form 3115 | If changing inventory or accounting methods |
Example: Seller Saved Thousands by Fixing MCF Reconciliation
A California-based beauty brand used FBA for Shopify orders but didn’t separate inventory SKUs. Result:
- Double reporting of sales
- Overstated revenue
- Understated fulfillment fees
Their CPA restructured their bookkeeping in January 2025:
- Mapped each Shopify order to FBA’s Multi-Channel Fulfillment report
- Added a connector tool to sync orders
- Recalculated accurate COGS by fulfillment channel
They saved over $7,800 in overstated income and filed a cleaner 2024 return.
Step-by-Step Guide for FBA + Shopify Sellers in 2025
Step 1: Enable Amazon MCF for Shopify
Use Amazon’s app or trusted integrations like Bytestand or WebBee.
Step 2: Assign Unique SKUs for Shopify Orders
Even if they’re fulfilled by Amazon, SKUs should be tagged separately from Amazon Marketplace SKUs.
Step 3: Track FBA Fees and Reimbursements
Download FBA reports monthly. Record:
- Fulfillment fees
- Shipping charges
- Lost/damaged item reimbursements
- Storage costs
Step 4: Reconcile Inventory Between Systems
Match beginning and ending inventory in both Shopify and Amazon. Update your books monthly.
Step 5: File Clean COGS and Avoid Double Income
Report correct COGS on Form 1125-A, and review Form 1099-K totals to avoid overreporting.
Conclusion
FBA can supercharge your Shopify store—but only if your books can keep up. In 2025, syncing platforms and tracking inventory across channels is the key to scaling without tax stress.
Call to Action
Running Shopify and using FBA for fulfillment? Need help with inventory sync, 1099-K issues, or clean COGS reporting?
Email Anshul Goyal, CPA EA FCA at anshul@kkca.io to clean up your books and stay audit-proof.
Disclaimer
This blog is for educational purposes only and does not replace legal or tax advice. Always consult a licensed CPA before making changes to your accounting or fulfillment process.
FAQs
1. Is Amazon FBA allowed for Shopify orders?
Yes—through Multi-Channel Fulfillment (MCF), but it must be integrated properly.
2. Should I track Shopify and Amazon SKUs separately?
Yes. Separate SKUs prevent inventory confusion and tax reporting issues.
3. Can I deduct FBA fees for Shopify orders?
Yes. All fulfillment, storage, and shipping costs are deductible under IRC §162.
4. Will I get two 1099-Ks?
Yes. One from Amazon, one from Shopify. Be careful not to double-report gross income.
5. What’s the biggest mistake with MCF sellers?
Failing to reconcile fulfillment fees and inventory between platforms, leading to profit and tax inaccuracies.
About Our CPA
Anshul Goyal, CPA EA FCA, is a U.S. Certified Public Accountant and IRS Enrolled Agent. He helps hybrid sellers who use Shopify and Amazon FBA set up integrated systems that track revenue, COGS, and fulfillment costs accurately—so they scale confidently and stay compliant.
Email anshul@kkca.io for a consultation.