Shopify bookkeeping for stores that take margins seriously
Shopify Payments, PayPal, Klarna, gift cards, refunds and chargebacks, reconciled into one honest P&L in your own QuickBooks or Xero file.
A Shopify store looks simpler to account for than a marketplace business. It isn't. Revenue arrives through three or four gateways on different payout schedules, discounts and gift cards muddy gross sales, and the official Shopify-QuickBooks connector is notorious for quietly mangling inventory and COGS.
We reconcile each gateway's payouts to Shopify's own reports, so what your books say matches what your dashboard says, and both match your bank. That reconciliation is the core of our Shopify bookkeeping service and the exact piece DIY setups skip. Hire a bookkeeper for a Shopify store without asking about gateway tie-outs and you'll get pretty reports built on the wrong revenue number.
If you've been searching for a bookkeeper for Shopify stores who actually understands the platform, that's the whole practice here. We handle outsourced bookkeeping for Shopify sellers end to end: online bookkeeping in your own file, accounting for Shopify Payments and every other gateway, 1099-K reconciliation at year end, and a Shopify accounting workflow your CPA can rely on. Bookkeeping for Shopify stores is not a sideline for us, and hiring an accountant for Shopify shouldn't mean teaching them the platform on your invoice.
Where Shopify books go wrong
Gateway soup
Shopify Payments settles daily-ish, PayPal holds funds, buy-now-pay-later providers pay on their own schedule. Each needs its own reconciliation. Mix them into one 'sales' line and you'll chase phantom discrepancies forever.
The connector problem
Auto-sync apps push order-level noise into QuickBooks until the file is unusable, and the inventory/COGS sync breaks in ways that are expensive to unwind. We use summary-level posting that stays reconcilable.
Discounts, returns and gift cards inflating revenue
Gross versus net matters. Gift card sales aren't revenue until redeemed, and a 30%-off sale that looks great in the dashboard can be margin-negative once fees and returns land. Your books should show that before you run the next one.
What we do every month
- Every gateway reconciled: Shopify Payments, PayPal, BNPL, more
- Payout-to-bank tie-out every month
- Gift card and store credit liability tracking
- Discount and refund reporting that keeps gross sales honest
- COGS on inventory movement with 3PL support
- Sales tax collected kept out of revenue
- Ad spend broken out by channel
- P&L, balance sheet and cash flow by the 10th business day
For DTC brands, dropshippers and hybrid sellers
A brand holding inventory in a 3PL needs landed-cost tracking and monthly inventory valuation. A dropshipper needs supplier-payment matching so COGS lands in the same month as the sale. A hybrid Shopify-plus-Amazon seller needs both, plus channel-level profitability. We set the file up for the business you actually run.
If you also sell on marketplaces, we consolidate everything into one set of books with per-channel P&L, which is the number that tells you where to put next quarter's effort.
Why not just use the Shopify P&L?
Shopify's analytics are sales analytics, not accounting. They don't know about your inventory purchases, payroll, software stack, or the loan payment. The dashboard answers 'how are sales?' Your books answer 'am I making money?' Those are different questions with different stakes.
Related services
Closed by day 10, or 50% off
Your prior month is reconciled and delivered by the 10th business day, guaranteed in writing. Miss it and that month's fee is half price. No competitor guarantees anything.
You own your books
We work inside your QuickBooks, Xero or NetSuite file, not ours. Leave any time and everything stays with you, diligence history included.
Exit-grade, always
Accrual books with landed-cost COGS and a maintained addback schedule. If a buyer or lender called tomorrow, your books would be ready.
Published pricing, no lock-in
Our full rate card is on the website and engagements run month-to-month. Every ecommerce-exclusive competitor hides pricing behind a sales call. We don't.
Shopify bookkeeping FAQs
Do I need a bookkeeper for my Shopify store?
At $100K+ a month with inventory, unquestionably. The gateway reconciliation and COGS work is where DIY and generalist books quietly fall apart, usually discovered at tax time, or worse, in diligence when a buyer reprices the deal over it.
QuickBooks or Xero for Shopify?
Both work well. QuickBooks Online is stronger for US sales tax handling; Xero is often cleaner for multi-currency. We work in whichever you have, and if you're starting fresh we'll recommend based on your setup, not a partnership commission.
Can you handle my 3PL and inventory?
Yes. We track inventory across locations including 3PLs, book landed costs properly, and run monthly valuation so COGS reflects what actually shipped.
What about Shopify's built-in tax reports?
Useful, not sufficient. Shopify tracks what it collected, but nexus analysis, filings and remittance still have to happen. We keep collected tax out of your revenue and work alongside sales tax filing tools or your filing provider.
How much does Shopify bookkeeping cost?
From $1,250/mo at the $100K-$250K monthly revenue tier, published on our pricing page instead of hidden behind a demo call. That's full monthly accounting: every gateway reconciled, COGS on inventory movement, per-channel P&L if you also sell on marketplaces, closed by the 10th business day. Month-to-month, no annual contract.
What does a Shopify accountant do each month?
Reconciles every gateway's payouts to Shopify's reports and your bank, books COGS from what actually shipped, tracks gift card liabilities, keeps collected sales tax out of revenue, and closes the file by the 10th business day with a video walkthrough. Your dashboard tells you sales. Your accountant tells you profit.
How do I record Shopify sales in QuickBooks?
Summary entries per gateway payout: gross sales, discounts, refunds and fees, with the deposit clearing the balance and gift cards parked in a liability account until redeemed. A2X or Link My Books posts it automatically. Per-order sync apps are the thing to avoid; they're the top reason Shopify QuickBooks files get abandoned and restarted.
Can you clean up my Shopify books?
Yes. If a connector app flooded your file or a previous bookkeeper booked payouts as revenue, we rebuild the affected months from gateway and Shopify reports at a flat quote, usually in one to three weeks. Cleanup then rolls into monthly service so the mess doesn't come back.
Cash or accrual for a Shopify store?
Accrual, because you carry inventory. Cash books expense a $60,000 stock order the month you pay for it, which wrecks that month's margin and flatters the next six. Accrual matches cost to the sale, which is the number you price by, borrow against, and eventually sell the company on.
When should a Shopify store hire a bookkeeper?
Once you're carrying real inventory and running more than one payment gateway, generally around $50K to $100K a month. Below that, disciplined DIY can hold. Above it, gateway reconciliation and COGS work take hours you don't have and punish errors you can't see. Most clients hire us about a year later than they wish they had.
We'll do last month's books free, and show you what your bookkeeper missed
The free Ecommerce Books Audit: connect read-only access and within 3 business days you get a clean month of books plus a 10-minute recorded teardown of every margin leak, COGS error and sales-tax risk we found. Keep it all, even if you never hire us.
- ✓ Books closed by day 10, guaranteed in writing
- ✓ Everything stays in your QuickBooks, Xero or NetSuite file
- ✓ Published pricing, month-to-month, no lock-in