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Shopify Payments deposits, app subscriptions, discounts, gift cards, and multi-channel sales all pull your numbers in different directions. We reconcile it all, so your Shopify books are clean and your real profit is clear.
Clean books are the difference between running your shopify business on real numbers and running it on guesswork. We give you accurate, up to date bookkeeping and clear reporting, so every decision, from pricing to hiring to your next investment, rests on what is really happening in your business, not a rough estimate at year end.
Why it is different
Shopify Payments nets fees before it deposits, apps bill on their own cycles, and discounts and gift cards distort revenue if they are not handled correctly. It is easy for a store to look profitable in Shopify and messy in the books.
We reconcile Shopify payouts to orders, separate fees and app costs, and handle discounts and gift cards properly, so your profit and loss matches what your store actually did.
What we handle
Shopify payouts matched to the orders and fees behind them.
Transaction fees and app subscriptions separated and recorded.
Discounts and gift cards handled so revenue is accurate.
Inventory and cost of goods tracked for true gross profit.
Sales tax organized across the states where you sell.
Clear reporting on what your store really earns.
Proven on Upwork
Since 2021, HOLO Bookkeeper has completed work for more than 1500 clients on Upwork and Fiverr, earning Top Rated status. Here is the kind of feedback shopify clients leave, and you can read the full portfolio and reviews yourself.
Cleaned up our Shopify books and separated all the fees and app costs. Now our margins make sense.
Shopify Store Owner · USA · Upwork ClientReliable monthly bookkeeping for our Shopify brand, with clear reports every month.
DTC Founder · USA · Upwork ClientSee the full Upwork portfolio and reviews → · Connect on LinkedIn →
How it works
Tell us about your business, your platforms, and where your books stand today.
We connect your accounts and tools with read only access wherever possible.
We build the right chart of accounts and catch up or clean up if needed.
Reconciled books and clear reports every month, plus automation where it helps.
Why choose HOLO Bookkeeper
You get the accuracy and dedicated attention of an in house bookkeeper, on demand, for only the work your shopify business needs, plus automation most in house hires never build.
QuickBooks ProAdvisor and Xero Certified Advisor with over 6 years and 1500+ clients.
You work with the person doing the work, with replies within 24 hours.
The same secure, certified process wherever your business is based.
We remove repetitive work with Excel, Sheets, and Python, so you pay for judgment.
Services and related industries
Related industries:
Free tools
Shopify accounting guide
Shopify makes selling easy, but the money reaches your bank in batches, net of processing fees, refunds and chargebacks, often across Shopify Payments, PayPal and other gateways. Clean Shopify bookkeeping rebuilds the full picture from those payouts.
Each Shopify payout combines many orders, minus fees and refunds. Your books should show gross sales, discounts, shipping income, sales tax collected, refunds and processing fees as separate lines, and each payout should reconcile to the bank. Apps like A2X, or a careful manual summary, make this repeatable. See our guide to Shopify fees, payouts and margins.
Shopify can calculate and collect sales tax at checkout, but on sales through your own store you generally register, file and remit it. Sales tax collected is a liability, not revenue. Once your sales into another state pass that state’s economic nexus threshold (often $100,000 in sales, and in some states a transaction count), you may need to register there. See sales tax nexus explained.
Product cost, inbound freight and packaging belong in cost of goods sold as items sell. Without that, gross margin is meaningless. Test pricing with the free profit margin calculator.
Gift cards sold are a liability until redeemed. Pre-order payments are customer deposits until shipped. Chargebacks and their fees need their own accounts so you can see what disputes are costing you.
If you also sell on Amazon, Etsy or wholesale, track revenue and fees by channel to see which one is really profitable. See Amazon seller bookkeeping.
General information as of 2026, not tax advice. Confirm sales tax and income tax treatment with your tax preparer.
Related guides
Questions and answers
Yes. We match payouts to orders and separate the fees Shopify nets before depositing.
Yes. We record discounts and gift cards correctly so your revenue is accurate.
Yes. App subscriptions are tracked and categorized as part of your operating costs.
Yes. If you also sell on Amazon or other channels, we handle the full picture.
QuickBooks or Xero, plus automation for higher volume stores.
Usually within a few days. After a short consultation we scope the work, agree a clear price, and begin, starting with catch-up or cleanup first if your books need it.
Yes. We work with shopify businesses in all 50 states, fully remotely, with the same secure and certified process everywhere.
Payouts are net of processing fees, refunds, chargebacks and sometimes reserves, and they can include orders from several days. Reconcile each payout to its orders and fees rather than matching totals directly.
Shopify can calculate and collect sales tax at checkout, but for sales on your own store you are generally responsible for registering, filing and paying it to each state where you have nexus.
Record gift card sales as a liability and move the amount to revenue when the gift card is redeemed.
Book a free 15 minute consultation and we will get your Shopify store’s books right.
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