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.
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.
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