Industries / Shopify
Shopify bookkeeping & accounting
Ben ran the close for JoyJolt as Controller — a DTC brand selling through Shopify, Amazon, and 15+ other channels on GoFlow. So the Shopify questions that usually stall a monthly close have already been answered here: which payout covers which orders, where the gift card liability sits, and why gross margin moved when nothing about the product did.
The Shopify gap
Your dashboard and your books are measuring different things.
Shopify shows you orders. Your bank shows you net deposits. Neither one is your P&L. When the two get stitched together by coding deposits to sales, revenue drifts, fees vanish, and refunds land in whatever month the money left — not the month the sale happened. Add a 3PL, inbound freight, and a few bundles, and inventory stops matching anything.
We rebuild the connection between the store, the gateways, and the ledger so the numbers you make decisions with are the same numbers your accountant files from.
What we actually do each month
Payouts reconciled to order activity
Gross sales, discounts, refunds, shipping income, tips, gift cards, and processing fees are each recorded — then the deposit is matched to what it actually settled.
One clearing account per gateway
Shopify Payments, PayPal, Shop Pay Installments, and anything else you accept each clear separately, so timing differences show up as timing differences instead of as mystery variances.
Sales tax kept off the P&L
Tax you collect is a liability, not revenue. We separate what marketplaces remit for you from what you file yourself so your returns and your books agree.
Landed cost in unit cost
Freight, duty, and inbound handling get capitalized rather than expensed on arrival. It's the difference between a gross margin you report and a gross margin you can price against.
Inventory and 3PL alignment
On-hand, in-transit, and 3PL quantities are reviewed against what the books say, with shrink and adjustments recorded deliberately instead of appearing as a year-end surprise.
Margin by product, not just by month
Contribution margin after landed cost, fees, shipping, and ad spend — so a discount decision or a freight increase shows up where you can respond to it.
Who you're working with
An operator, not an outsourced inbox.
Ben's background is retail and logistics before it was advisory: accounting at Adorama, accounting at a freight-forwarding company, then Controller at JoyJolt. Freight is where the landed-cost habit comes from — once you've allocated duty and freight across a container, you stop treating COGS as a plug.
Practically, that means we ask about your product flow first: where units land, who holds them, how bundles are built, what your inbound cost actually includes. Then we build books that answer those questions every month without you chasing anyone.
Selling on marketplaces too? Here's how we handle Amazon.
FAQ
Shopify accounting questions we get asked
- Why doesn't my Shopify payout match my Shopify sales number?
- Because the payout is net. Shopify Payments takes processing fees out before the deposit, refunds and chargebacks come out of later payouts, and gift cards, tips, shipping, and sales tax all move separately. We reconcile the payout to the underlying order activity so both numbers exist and both are right.
- Do you handle Shop Pay Installments, PayPal, and third-party gateways?
- Yes. Each gateway settles on its own schedule with its own fees, so each one gets its own clearing account and its own reconciliation. Mixing them into one undeposited-funds bucket is a common reason a balance sheet stops tying out.
- Can you make gross margin accurate if we sell bundles and kits?
- Yes, but it takes a real cost build. Kits and bundles need component-level costs, and inbound freight and duty need to be capitalized into unit cost. Once that's in place, margin by product and by bundle holds up month to month.
- We sell wholesale and DTC out of the same store. Can you separate them?
- That's a chart-of-accounts and mapping question, and yes. Wholesale usually needs AR, terms, and different margin expectations than DTC, so we track them as distinct revenue streams instead of one blended line.
- Which apps do you work with?
- We work with the stack you already have and only suggest changes when they earn their keep. On the ecommerce side that's typically QuickBooks with a settlement tool like A2X or ConnectBooks, plus your 3PL or inventory system as the source of unit movement.
- How fast is your monthly close?
- We target 5–7 business days after month-end and we tell you the date up front. Predictable timing matters more than speed records — you should know when the numbers land before you need them.
Related: All industries we serve·Amazon seller bookkeeping·Ecommerce bookkeeping services·Fractional CFO for ecommerce·Tools we implement·A2X vs ConnectBooks
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