WooCommerce orders are gross and payouts are net. Post each order with its coupon, shipping and sales tax apart.
When the bank never balances against your WooCommerce sales, the gap is fees, refunds and payout timing. Intuit's free WooCommerce Connector by QuickBooks imports each paid order. Autymate builds the WooCommerce to QuickBooks Online integration around your chart of accounts: coupons, shipping and sales tax post to the accounts your team picks, bank-transfer orders wait until the money arrives, and each store posts to its own QuickBooks class, location or company. Autymate connects WooCommerce, QuickBooks and 300+ other tools.
Yes, you can integrate WooCommerce with QuickBooks Online using Autymate. Intuit also offers a free WooCommerce QuickBooks connector, the WooCommerce Connector by QuickBooks, which imports each paid order as a sales receipt or an invoice. When you connect WooCommerce to QuickBooks with Autymate, the integration follows your accounting rules: which income account each product posts to, where coupons, shipping and tax go, which store posts to which company or class, and what waits for review.
Each WooCommerce order already holds what your books need: status, coupon, shipping, tax by rate and gateway.
WooCommerce marks an order Processing when it is paid and Completed when it is fulfilled, so Processing is where the sale happened. On hold means a bank transfer or cheque is still on its way, and Pending payment means nothing has been paid yet. Which statuses post is a revenue decision your team makes once.
Each line keeps its price before and after discounts, each coupon carries its own code and amount, and shipping arrives as a line of its own with its own tax. Post the pre-discount price without the coupon and sales are overstated; post only the order total and shipping income hides inside product revenue.
WooCommerce stores tax per rate, so a Quebec order can carry GST and QST as two tax lines, and a store can price with tax included or added at checkout. Intuit's connector maps WooCommerce tax rates for companies outside the US and hides tax mapping by default for US companies.
A refund is a record of its own, with its own date and the lines, tax and shipping it returns. A partial refund leaves the order's status unchanged, and a manual refund only records the refund in WooCommerce without sending any money back. WooPayments keeps its processing fee when you refund.
WooPayments takes its fee from each order and pays out daily by default, two business days later, net of fees and refunds. The Stripe gateway records a Stripe Fee and a Stripe Payout on each order, and PayPal Payments records its PayPal Fee and PayPal Payout the same way. That is why a payout never equals one day's orders.
Intuit's connector can send stock levels from QuickBooks to WooCommerce, but two-way WooCommerce QuickBooks inventory sync is not offered yet, so stock changes are made in both systems. QuickBooks Online tracks inventory on its Plus and Advanced plans. Pick one system to own stock counts, so the two never disagree.
Each WooCommerce store is its own WordPress site, with its own orders, order numbers and payouts.
Every store posts on the same product, coupon, shipping, tax and gateway rules, so a new brand site starts from a mapping your team already approved. Each site numbers its orders on its own, so two stores can send the same order number; Autymate adds a store prefix that keeps them apart.
Your wholesale site sells to trade customers and maps its orders to Wholesale Sales, while the retail stores keep Product Sales. Each difference is approved once and stays with the store that needs it.
Stores owned by one company post to one QuickBooks company, each tagged with a class or location, so each brand has a profit and loss. Each WordPress site also runs a separate WooPayments account, so payouts stay apart.
When a brand belongs to a separate legal entity, its store posts to that entity's own QuickBooks company, on the same mapping template as the others.
Product, coupon, shipping, tax and gateway lines each post to an account your accountant names.
| Source | Destination | Example |
|---|---|---|
| Product or variation SKU | QuickBooks item and income account | HOODIE-BLK-M → Hoodie (Apparel Sales); MUG-12 → Mug (Homeware Sales) |
| New or unmapped SKU | Held for review | An order for a SKU with no mapping waits for your team instead of creating a stray item. |
| Paid order (Processing) | Sales receipt | Posted on the date WooCommerce recorded the payment, or as one entry per store per day. |
| Wholesale order on terms | Invoice against Accounts Receivable | Autymate posts trade orders when they are placed, so they reach QuickBooks before they are paid. |
| Coupon | Discounts Given | WELCOME10 → Discounts Given, so product sales stay at full price. |
| Shipping charged | Shipping Income | Kept apart from product sales, with its own tax where the store charges it. |
| Tax line by rate | Sales Tax Payable | Posted as WooCommerce collected it, rate by rate. |
| Payment method | A clearing account per gateway | WooPayments → WooPayments Clearing, in place of Undeposited Funds; PayPal → PayPal Clearing; bank transfer → the bank. |
| Gateway fee | Merchant fees expense | Autymate posts one line per fee, so sales stay at gross. |
| Refund or partial refund | Refunds and returns | Dated when WooCommerce issued it, with the lines and tax it returned. |
| Gift card sold | Gift Card Liability | Autymate books it as money owed until a customer spends it. |
| Store | Class, location or company | Retail site → Class: Retail; Trade site → Class: Wholesale; Outdoor brand → its own company |
| Orders before go-live | Left as they are | Orders from your go-live date onward post; earlier history stays where it is. |
One evening in a WooCommerce store, followed from checkout to the September close.
"So my bank will never balance," one store owner wrote in 2023. Our example store takes three card orders through WooPayments on Wednesday 30 September: $280.36 in all, with one coupon, shipping and sales tax.
$250.00 of product sales, less an $8.00 coupon, plus $19.00 of shipping income and $19.36 of sales tax owed: $280.36. That is the store's September, and none of it is a deposit yet.
WooPayments keeps 2.9% plus 30¢ on each order: $2.73 on order A, $4.29 on B and $2.01 on C. That is $9.03 in fees, leaving $271.33 to pay out.
Order C was placed at 9:30 pm Eastern. WooPayments starts each new day at midnight UTC, which is 8 pm Eastern, so it counts C as a 1 October sale. Its September shows $221.36 of sales; the store's shows $280.36.
Two business days later, orders A and B are paid out together as $214.34 on Friday the 2nd. Order C follows alone as $56.99 on Monday the 5th. Together: $271.33.
Your October payout report shows $214.34 and $56.99, and neither equals any one order. At the September close, $271.33 is earned but not yet paid out; a WooPayments Clearing account holds it as an asset until the two payouts empty it. A $32.40 partial refund on Tuesday the 6th belongs to October, and order B's $4.29 fee is not returned.
The situations a WooCommerce QuickBooks sync meets every month, and how each one is handled.
| Situation | What it means in QuickBooks | How Autymate handles it |
|---|---|---|
| Payouts that are net of fees and refunds | Each payout is smaller than the orders it covers and mixes several of them, and late-evening orders on the 30th or 31st are paid out in the next month, so "find match" finds nothing. | Autymate posts each fee once to your fees account and clears each payout against WooPayments Clearing, so every deposit has a match. |
| A plugin update or a lost API key stops the orders | Nothing posts and nothing warns you, until the bank and the books disagree at month-end. | Autymate's team monitors your runs, and Autymate flags a store whose orders stop arriving, so a silent plugin is caught early. |
| An order for a SKU nobody mapped | The product arrives as a new item or a default one, such as "Default for Unmatched Products", and sales by product drift from the store's. | Held for review with the SKU. Once your team maps it, every later order for that SKU posts on its own. |
| An order with a tax rate QuickBooks has no code for | VAT, GST or QST lands on the wrong code, or someone fixes the rate by hand on every transaction. | Held for review with the rate. Autymate maps each WooCommerce rate to its QuickBooks tax code, so later orders at that rate post on their own. |
| A bank-transfer order still On hold | Stock is already reduced, but no money has arrived and nothing is in QuickBooks yet. | Autymate holds it until WooCommerce marks it paid, or posts it as an open invoice, whichever your team prefers. |
| A partial refund after the month is closed | The refund belongs to the month it was issued, and the processing fee on the original order is not returned. | Posted on its own date against revenue, with a reference back to the WooCommerce order. |
| The store and a bank or PayPal feed both record the sale | The order is booked as income and the deposit is added as income again. | Autymate gives each sale one source, so the deposit is matched, not added. |
| Moving off OneSaas or another plugin | A start date that overlaps orders already imported posts the same months twice. | Autymate starts posting after the last order the old tool posted, so no month posts twice. |
WooCommerce QuickBooks automation with five checks between a customer's checkout and your monthly close.
Each variation's SKU has to match an approved QuickBooks item before its order posts. A product launched on Friday waits for one mapping, not a cleanup at month-end.
Only the statuses your team chose post as sales, so On hold and Pending payment orders wait. Autymate posts full and partial refunds on the same rules.
Deduplication checks each order and refund against what Autymate has already posted, including after a store's connection is restored.
An order the rules cannot place, such as an unmapped tax rate or a gateway with no clearing account, waits with a note on what to check. Your team makes the call.
Autymate's team monitors your runs, so a site that goes quiet after a plugin update is flagged early instead of found at month-end.
Four ways to run a WooCommerce QuickBooks sync, compared on what month-end still asks of your team.
| Path | Best fit | What your team still owns |
|---|---|---|
| WooCommerce Connector by QuickBooks | One store with orders paid at checkout | Matching WooPayments, Stripe or PayPal payouts to orders, any order not yet paid, and stock changes in both systems |
| A WooCommerce marketplace plugin | A single store that wants more settings or faster syncing, on a free tier or a paid plan | Configuring the plugin, keeping it working through WordPress and WooCommerce updates, and checking what it posts |
| A custom build on the WooCommerce REST API | A developer team with stable requirements and time to maintain it | Authentication, webhooks that switch off after five failed deliveries, QuickBooks API logic, retries, and every change after launch |
| Autymate | Several stores or entities, wholesale orders on terms, or an order volume too high to check by hand | Signing off the blueprint and deciding each held order, while Autymate matches each payout to its orders |
One store feeds one QuickBooks company, every order is paid at checkout, and someone is happy to match payouts to orders by hand.
Several stores or brands need their own class or company, wholesale customers buy on terms, or coupons, shipping and tax need to post by rule across every store, with anything unplaced held for review.
Running one store with orders paid at checkout? Intuit's free connector may be all you need. Talk to us when a second store, a wholesale site or a second company joins.
Before your WooCommerce to QuickBooks Online integration runs live, a real month of your orders goes through it.
Each WordPress site with its gateways and plugins, your QuickBooks plan and companies, and whether Intuit's connector, a plugin or a bank feed already records the sales.
Which order statuses post as sales, how On hold bank transfers are treated, and which refunds come across.
SKUs to income accounts, coupons to discounts, shipping to shipping income, tax by rate to Sales Tax Payable, and each gateway to a clearing account of its own.
One sales receipt per order, or one entry per store per day. Choose too whether Autymate posts fees, refunds and payouts as well.
Last month's orders, coupons, partial refunds and any payouts in scope run through the mapping, checked against WooCommerce and your gateway reports.
Orders post from the agreed date, store by store, and an order the rules cannot place sits in a review list until your team decides.
WooCommerce sellers with several sites, wholesale terms or subscriptions, where a WooCommerce accounting integration earns its keep.
Three orders with a coupon, shipping and tax are paid out as two payouts, days apart. Sales, discounts, shipping income and tax each post to their own account.
Trade customers buy on 30-day terms, and Intuit's connector cannot import an unpaid order. Autymate posts wholesale orders as invoices against Accounts Receivable.
A store per brand, country or currency, each with its own payouts and order numbers. Opening the next site means approving its differences, not rebuilding the mapping.
WooCommerce Subscriptions creates a renewal order every billing cycle, and a failed renewal is retried for about a week. Autymate posts each renewal once it is paid and releases annual plans from deferred revenue on the schedule your accountant sets.
WooCommerce QuickBooks automation built around how your stores sell, and checked against your own orders before launch.
Trade orders reach QuickBooks as invoices before they are paid.
Discounts Given shows what your coupons cost, apart from product sales.
Every posted entry carries a reference to its source: the WooCommerce order, or the store's day.
Held orders wait for your decision, with Autymate's support on hand.
Yes, the WooCommerce Connector by QuickBooks is free, according to Intuit's QuickBooks App Store listing, and Intuit builds it.
Marketplace plugins vary: MyWorks has a free tier for up to 20 orders a month and paid plans above that, and WP Swings sells its extension on the WooCommerce Marketplace. Autymate's cost depends on your stores, entities and order volume, and is set out in your integration blueprint.
To connect WooCommerce to QuickBooks Online yourself, install Intuit's free WooCommerce Connector by QuickBooks from inside QuickBooks Online, link your store, choose which order statuses to import and pick a start date up to 12 months back.
With Autymate, the WooCommerce accounting integration is mapped to your chart of accounts first, tested on a real month of orders, then switched on from your go-live date, after the last order any earlier tool posted, so nothing posts twice.
As a sales receipt when the order is paid, or as an invoice with a separate payment.
Intuit's connector offers both, matches products on the WooCommerce SKU, brings refunds in as refund receipts, and lets you choose which order statuses it collects. WooCommerce marks an order Processing when payment arrives, so Processing, not Completed, is usually the status that should post. With Autymate, your team picks the record type and the statuses that post in every store.
Record the full order as the sale and the fee as an expense.
WooPayments charges 2.9% plus 30¢ on a US card order and keeps that fee when you refund. Intuit's connector imports order fees as an expense with each sales receipt, and the Stripe gateway and PayPal Payments record the fee on the WooCommerce order. With Autymate, each fee posts once to your fees account and the sale stays at gross.
A payout is the net of several orders.
WooPayments pays out daily after two US business days, takes its fee from each payment, deducts refunds and disputes, and starts each day at midnight UTC, so an evening order can join the next day's payout. Intuit says payout-level reconciliation for its WooCommerce connector is planned for a future release, so today the matching happens outside the connector, which is where Autymate matches each payout to its orders.
Usually because two things record the same sale: a WooCommerce QuickBooks sync creates the invoice or sales receipt, and a bank, PayPal or Stripe feed adds the same money as income.
One store owner called the result "2x revenue" in 2023. Match the deposit to the sale already in QuickBooks instead of adding it. With Autymate, each sale has one source, and deduplication checks what has already posted, so nothing posts twice.
Common causes are a WordPress or WooCommerce update, a plugin that is not yet compatible, or an API key tied to a user who was later deleted.
WooCommerce also switches a webhook off after five failed deliveries in a row. Nothing warns you until the bank and the books disagree. With Autymate, a store whose orders stop arriving is flagged, and Autymate's team monitors every run.
Not with Intuit's connector today.
Its help says the new e-commerce connectors don't yet offer two-way inventory sync, so stock changes are made in both systems, and the connector can only send stock levels from QuickBooks to WooCommerce. Intuit's older connector warned that sending stock before QuickBooks holds stock levels could wipe out WooCommerce stock levels. Pick one system to own stock counts. With Autymate, your team picks that system and Autymate keeps the other one in step.
Intuit replaced the OneSaas WooCommerce connector with the WooCommerce Connector by QuickBooks, which runs inside QuickBooks Online.
The new connector syncs every few hours rather than hourly and imports up to 12 months of history. Intuit warns that a start date overlapping orders already imported creates duplicates, so start after the last order your old connector or plugin posted. With Autymate, posting starts after that last order, so no month is imported twice.
Not through Intuit's connector today.
Its help says the new connectors can't import orders as unpaid, and a sales receipt waits until the order is fully paid. That keeps bank transfers on hold and trade orders on terms out of QuickBooks until they are paid. With Autymate, they post as invoices against Accounts Receivable when the order is placed, so each trade sale lands in the month it was made.
Yes, you can connect multiple WooCommerce stores to QuickBooks: each store is its own WordPress site with its own orders and payouts, and Intuit allows more than one connection to the same service.
With Autymate, each store posts to its own class or location in one QuickBooks company, or to its own company when it belongs to a separate entity, on one shared mapping template with approved differences.
Intuit's connector covers the common case: one store, orders paid at checkout, payouts matched by hand.
Autymate fits when a wholesale site needs invoices before payment, a second brand needs its own profit and loss, or every store's orders need watching, not just the one you check. In those cases, Autymate's WooCommerce QuickBooks integration keeps routine orders posting on rules your team signed off, and an order that needs a decision waits for one.
Bring one month of orders and your chart of accounts. We will show you how to connect WooCommerce to QuickBooks so every store, coupon and refund lands where it should, then plan your WooCommerce to QuickBooks Online integration around it.
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