Bookkeeping for Retail & E-Commerce
For Houston retail owners, Shopify sellers, Amazon operators, and multi-channel brands who need real gross margin, real inventory numbers, and sales tax that doesn't blow up at year-end.
The bookkeeping problems specific to your industry
Merchant deposits don't match sales
Stripe, Square, Shopify Payments, and Amazon all net out fees and refunds before depositing. Without careful reconciliation, gross revenue and fees are hopelessly tangled.
Inventory is a black box
Booking every purchase as an expense inflates COGS in month one and understates it later. You need real inventory accounting to see actual gross margin.
Multi-state sales tax
Selling online means economic nexus in states you've never set foot in. Missing filings turns into penalties fast.
Marketplace and channel splits
Amazon, eBay, Etsy, TikTok Shop, and your own site each report differently. Blending them into one P&L hides which channel actually makes money.
Returns, chargebacks, and refunds
These have to be netted against revenue in the right period — otherwise your P&L swings wildly month to month for no real business reason.
Loan or line of credit
Lenders and inventory-financing companies want clean financials that show real gross margin and inventory turnover. Most retail books can't produce that.
Industry-specific patterns we clean up regularly
- Shopify / Amazon / eBay revenue booked at the gross payout instead of gross sales minus platform fees, refunds, and chargebacks — revenue looks lower than reality.
- Sales tax on the Shopify order settled by Shopify Tax or a Marketplace Facilitator, but still booked as a liability owed by the store — double-counted.
- Inventory tracked by piece count in Shopify but never reconciled to a QuickBooks inventory asset, so COGS is a plug figure.
- In-store POS (Square, Clover, Lightspeed) and online store deposits hit the same bank account and get combined in QuickBooks.
- Amazon FBA storage, referral, and fulfillment fees dumped into one 'Amazon Expense' category, hiding which SKUs are profitable.
- Refunds and returns netted against sales instead of tracked as a separate contra-revenue account, distorting return-rate visibility.
Multi-channel boutique reconciling Shopify + POS + Amazon before an SBA line of credit
Illustrative composite based on the type of engagement we handle. Not a specific client.
A Houston boutique sold through a physical store, a Shopify site, and an Amazon Handmade shop. Their books used one 'Sales' account, expensed inventory at purchase, and never split platform fees out of gross revenue. When they applied for an SBA line of credit, the underwriter asked for channel-level revenue and gross margin — the QuickBooks file could not produce it.
Outcome: We integrated Shopify and Amazon with automated daily-summary journal entries, split gross sales / fees / refunds / sales tax into separate accounts per channel, converted inventory to a tracked asset with monthly COGS, and reconciled 14 months. Channel-level margin came in at 62% online / 44% Amazon / 55% in-store — the line of credit was approved on the strength of that transparency.
A bookkeeping system built for Retail & E-Commerce
- QuickBooks setup with inventory tracking
- Shopify / Amazon / Square reconciliation
- Channel-level revenue reporting
- Multi-state sales tax coordination
- Merchant fee reconciliation
- Returns & chargeback handling
- Real gross margin reporting
- Dedicated bookkeeper, monthly close
Bookkeeping across Houston & by industry
Monthly bookkeeping, cleanups, loan-ready financials and QuickBooks setup.
Compare bookkeeping playbooks for contractors, retail, legal, healthcare, and real estate.
Neighborhood-by-neighborhood bookkeeping coverage across the Houston metro.
What lenders want to see in your books before approving an SBA 7(a) or 504 loan.
Common questions
Do you integrate with Shopify or Amazon?
Yes. We use A2X, Synder, or direct QuickBooks integrations to bring settlement data in cleanly — separating gross revenue, fees, refunds, and payouts so your P&L reflects reality.
Can you help with multi-state sales tax?
We coordinate with a sales tax filing service (Avalara, TaxJar, or similar) and make sure QuickBooks matches what they file. If you're not registered where you should be, we'll flag it.
How do you handle inventory?
For most SMB retail clients we use QBO's inventory tracking or a Shopify-native inventory system, and reconcile monthly. For larger volumes we integrate with a dedicated IMS.
Let's talk about your books.
Free 30-minute consultation. No sales pressure — just a clear look at where your books stand.