The ecommerce accounting stack
For most service businesses or single-channel retailers, “accounting software” is one product. For ecommerce sellers, it is rarely just one. The typical ecommerce stack has three or four layers, and which layer matters most depends on your channel mix and volume.
- • Marketplace / storefront. Shopify, Amazon Seller Central, Etsy, eBay, Walmart Marketplace, your own ecommerce site. The system of record for orders, customers, and listings.
- • Integration layer. A2X, Link My Books, Synder. Reads marketplace settlement data, parses orders, fees, refunds, advertising spend, posts summary journal entries to accounting.
- • Accounting software. The general ledger. QuickBooks Online or Xero is most common for small ecommerce sellers in the United States.
- • Inventory management. Cin7, Linnworks, ShipStation, Shipbob, others. For multi-channel sellers, often the system of record for stock-on-hand. Pushes summary inventory values to accounting.
Feature priorities for ecommerce
Multi-channel order import
If you sell on more than one channel, the integration layer must handle each. A2X is strongest for Amazon and Shopify; Link My Books has broad multi-channel support; Synder is broader still. Verify that the integration handles your specific channels before committing to an accounting product.
Marketplace fee separation
Marketplace fees (Amazon FBA fees, Shopify transaction fees, Etsy listing and transaction fees, payment-processor fees) should land in distinct expense accounts so you can see your true margin. The integration layer parses these out of settlement data and posts them correctly.
Inventory sync
Stock-on-hand updated across channels in real time so you do not oversell. Above modest volume, this is usually a separate inventory tool, not the accounting software.
Sales tax across jurisdictions
Marketplace facilitator laws shift collection to the marketplace for many sales, but your direct-to-consumer storefront sales remain your responsibility. Automated sales-tax software is usually warranted past modest multi-state volume.
COGS by product
Per-SKU COGS is the only way to see per-product profitability. The accounting software calculates this from the costing method (FIFO or average) and the sales feed; getting this right depends on the integration layer correctly classifying each marketplace transaction.
Returns and refunds handling
Returns reduce gross sales and (for accrual sellers) reverse COGS. The integration layer should handle returns automatically; the accounting software should accept them as contra-revenue plus inventory adjustments.
Category recommendations
| Category | Fit | Why |
|---|---|---|
| Free / low-barrier | Not the fit | Insufficient inventory and marketplace-integration support for any meaningful ecommerce volume. |
| Mainstream small-business cloud (plus integration layer) | Strong fit | Default fit for most ecommerce sellers. Pair QuickBooks Online or Xero with A2X / Link My Books / Synder, and an inventory tool if multi-channel. |
| Ecommerce / inventory specialist | Strong fit | Right category for higher-volume multi-channel sellers. Tools like Cin7 sit between marketplaces and accounting and replace the separate integration layer for some sellers. |
| Service-business specialist | Not the fit | Inadequate for any inventory-bearing business. |
| Mid-market | Acceptable fit | Right category if ecommerce is multi-entity (multi-country operations, multiple LLCs) or you have B2B wholesale at scale alongside DTC. |
| Managed bookkeeping services | Acceptable fit | Some managed bookkeeping services specialise in ecommerce (Bookkeeper360, Bench's ecommerce offering). Verify multi-channel and integration-layer fluency before committing. |
Frequently asked questions
Why do I need an integration layer between my marketplace and my accounting software?
Because marketplace data is messy. Amazon, for example, deposits a single biweekly settlement amount that bundles dozens of orders, refunds, fees, advertising spend, and reserves. If you put the deposit straight into accounting as a single line, you cannot calculate gross sales, you cannot reconcile fees, and you cannot calculate accurate COGS. The integration layer (A2X, Link My Books, Synder, others) parses the settlement, posts the appropriate journal entries, and reconciles to the deposit. Without it, ecommerce books are unreliable.
Do I need separate inventory management software in addition to accounting?
Below 200 SKUs and a single channel, the inventory built into mainstream cloud accounting is usually sufficient. Above 200 SKUs or across multiple channels, dedicated inventory-management software (Cin7, Linnworks, ShipStation, Shipbob, others) handles real-time stock levels and channel sync better than accounting. The inventory tool then feeds aggregate values into accounting.
How does multi-state sales tax work for online sellers?
After Wayfair (2018), states can require out-of-state sellers to collect tax based on economic-activity thresholds (commonly $100k or 200 transactions per state). Marketplace facilitator laws shift the collection burden to the marketplace itself for most sales (Amazon, Etsy, Walmart usually collect for you). Direct-to-consumer sales through your own Shopify store remain your responsibility. Automated sales-tax software (Avalara, TaxJar) reads from your accounting and files the returns.
Should I track every individual order in my accounting software?
Almost never. The right pattern is to track summary entries by day or by settlement period. Per-order detail belongs in the marketplace itself or in the inventory-management tool. Posting every order to accounting bloats the general ledger, slows everything down, and obscures the financial picture. The integration layer's job is to summarise without losing the ability to drill back into source data when needed.
How do I handle returns and refunds in the books?
Returns reduce gross sales and (for accrual basis) reverse the COGS associated with the returned item. Most ecommerce integration layers handle this automatically: when a return shows in the marketplace data, it posts a contra-revenue entry plus a COGS reversal. Cash-basis sellers can simply net returns against sales for the period. The category to watch is restocking fees and damage adjustments, which need their own GL accounts.
Related guides
Companion pages on this site and on our portfolio of independent pricing references.
When inventory is the deciding feature, including levels of inventory tracking and SKU thresholds.
If you sell internationally, multi-currency support is the second most important feature after inventory.
Retail chapter, including POS integration.
Single-member LLC chapter for sole owners; multi-member if you have a business partner.
S-Corp chapter, often relevant for ecommerce sellers past $50k net income.