Turn every shipped ShipStation order and the shipping your buyer paid into QuickBooks Online entries, store by store.
ShipStation already sends shipped orders to U.S. QuickBooks Online accounts as sales receipts or invoices. Autymate's ShipStation QuickBooks Online integration picks up what that sync leaves for month end: shipping income on its own line, each label's cost posted against its order, and every store posting to the right company or class.
Yes, you can integrate ShipStation with QuickBooks Online using Autymate. ShipStation's own integration, for U.S. QuickBooks Online accounts, sends each shipped order once as a sales receipt or an invoice, with the shipping the buyer paid added to the last product line. With Autymate, the ShipStation QuickBooks integration also books shipping income on its own line, posts each label's cost against its order, routes each store to its company or class, and holds unmatched orders for review.
Six things ShipStation knows about each order and label decide what reaches QuickBooks.
ShipStation imports orders from every store and sends one to QuickBooks only once it reaches Shipped, numbered SS plus ShipStation's order ID, with the Order # in the record's statement memo or message. ShipStation's help center says each order "will be processed once and only once". A split order reaches Shipped only when its last box ships.
Each Shopify, Amazon, eBay, Etsy, WooCommerce or wholesale connection is a store in ShipStation. The native integration sends every store, or the ones you pick, through one connection's settings. Brands and ship-from locations shape labels and packing slips, not the books, so a two-brand seller sees both brands in the same accounts.
The native integration searches QuickBooks by SKU and creates a non-inventory item when nothing matches. A product name already used with a different SKU becomes a second item with an SS prefix. Non-inventory items carry no quantity on hand and no cost of goods sold, so an Amazon SKU, a Shopify SKU and a gift-set kit for the same candles can end up as three new items.
These are two different numbers. Shipping Paid is what the buyer was charged; Shipping Cost is the carrier fee for the label, and ShipStation's Shipments report subtracts the label and insurance cost from Shipping Paid in its Difference column. On a free-shipping order Shipping Paid is $0.00, so the label is the whole difference. Through ShipStation's own integration, only Shipping Paid travels with the order to QuickBooks.
Labels bought through ShipStation Carriers come out of a prepaid ShipStation balance, topped up from a bank account or card, while your own UPS or FedEx account bills you monthly. Carrier adjustments for weight, size or address are debited after the parcel ships, with a processing fee of 20% of the adjustment, $0.50 minimum and $5.00 maximum per shipment. A voided ShipStation Carriers label can take up to 21 business days to be credited back.
The native integration matches customers by the order's email and maps tax to agencies by the buyer's state, using agencies already set up in QuickBooks. ShipStation does not collect the buyer's payment: Shopify Payments, Amazon, PayPal or your processor does, and pays out net of fees across many orders at once. In states with marketplace facilitator laws, Amazon, eBay and Etsy collect and remit the sales tax themselves.
With Autymate, each ShipStation store posts to its own QuickBooks company, class or income account.
In this sample setup, Harbor & Wick sells candles through its Shopify store, on Amazon (orders it ships itself) and through a wholesale store, and its sister brand Tidewater Soap Co. is its own LLC and files its own returns. One ShipStation account ships for both brands. The store an order came from decides its QuickBooks company, so Tidewater's orders reach Tidewater's books while ShipStation still prints every label.
A gift set is the same product whether it sells on Shopify or Amazon, even when each channel spells its SKU differently. Each SKU and alias points at one QuickBooks item in every company file, and shipping income and shipping costs use the same accounts in each. When Harbor & Wick adds a Walmart store, its orders use the group's existing accounts from the first sale.
Harbor & Wick's wholesale store sells to gift shops on 30-day terms, so its orders post as invoices to Accounts Receivable instead of as sales receipts, and its case-pack SKUs point at wholesale items on Wholesale Sales, because a QuickBooks item carries one income account. Everything else matches the retail stores: the same shipping income account and the same treatment of label costs.
Inside one company file, each store becomes a class, so the profit and loss report can be run for Shopify, Amazon and wholesale side by side, and each channel's margin after shipping shows without a spreadsheet. ShipStation's own integration sends every store into the same income accounts. Plus allows 40 classes and locations between them; Advanced sets no limit.
Each part of a shipped order maps to one QuickBooks account, item, class or company.
| Source | Destination | Example |
|---|---|---|
| Shipped order from a Shopify or marketplace store | Sales receipt deposited to that channel's clearing account | Shopify order → Clearing |
| Order from the wholesale store | Invoice in Accounts Receivable, on the customer's terms | Wholesale → A/R |
| Store or channel | Class in the brand's QuickBooks company | Amazon → Class |
| Brand that is its own legal entity | Its own QuickBooks company file | Tidewater → Own company |
| SKU or channel alias | One existing QuickBooks Product/Service, never a new non-inventory item | HW-GIFT-3 → Gift Set |
| Kit or bundle SKU | The QuickBooks item or items your accountant picks | Trio kit → Chosen item |
| Item price times quantity | Product Sales, by category if finance reports it that way | 2 × $24.00 → Product Sales |
| Shipping Paid | Its own line on Shipping Income | $7.95 → Shipping Income |
| Discount or promo code line | A discount line on Sales Discounts | WELCOME10 → Discounts |
| Order tax | Sales tax as the order carries it, with marketplace-remitted tax kept apart from the tax you owe | Amazon tax → Kept apart |
| Label Shipping Cost and Insurance Cost | Your shipping expense account, against the order that used the label | $6.40 → Postage Expense |
| Buyer name and email | Customer by the rule your accountant picks, such as one customer per marketplace | Amazon buyer → Amazon Sales |
| Store order number, ship date and tracking number | A reference on the QuickBooks record back to the ShipStation order | #4417 → Reference |
How much detail QuickBooks keeps depends on volume and payouts; your accountant chooses before any order posts.
Every shipped order becomes its own sales receipt or invoice, with its customer, items and order number, the shape ShipStation's own integration uses. Wholesale accounts on terms need this, because each invoice is collected on its own, and it reads well at a few dozen orders a day. At thousands of orders a month, the customer list and the deposit screen fill with one-off records.
One sales receipt per store per day, split into product sales, shipping income, discounts and tax, with the day's order numbers kept as its reference. A payout is matched against a few summaries instead of hundreds of receipts, and each store's day still ties back to ShipStation order by order.
Shopify and marketplace orders post as a daily summary per store, while wholesale orders post one invoice each, because each is billed and collected separately. Harbor & Wick uses this design in the worked example below.
A sample Shopify order, followed from ShipStation to QuickBooks to the payout in the bank.
Shopify order #4417 from Harbor & Wick's store is paid on October 5 and ships on October 6 to Portland, Oregon, where no sales tax applies. It holds a candle gift set at $48.00, a wick trimmer at $12.00 and $7.95 of shipping, $67.95 in all. Shopify Payments took the card payment, so ShipStation only knows what was sold and shipped.
Sent natively, the $7.95 would be added to the wick trimmer's line, so Product Sales would read $67.95 and Shipping Income nothing. Autymate adds the order to the Shopify store's October 6 summary as $60.00 of Product Sales and $7.95 of Shipping Income, and checks the summary against the day's ShipStation order totals before it posts.
The Shopify store's summary for October 6 is a sales receipt deposited to Shopify Payments Clearing, not to the bank, and order #4417 adds $67.95 to it. The receipt carries the day's Shopify order numbers, so any line on it traces back to the order your team would search for.
The ShipStation shipping cost QuickBooks receives for #4417 is its $6.40 USPS label, which Autymate reads from ShipStation and posts to Postage Expense with the order's reference. Shipping Paid less Shipping Cost leaves $1.55, the figure in the Difference column of ShipStation's Shipments report. On October 21 a $1.10 carrier adjustment for package size comes off the balance with a $0.50 processing fee, and the bookkeeper records the $1.60 from ShipStation's balance report to Postage Adjustments. The order that made $1.55 on shipping on October 6 lost $0.05 on it by October 21.
Shopify Payments pays out on October 8, less its processing fees, in one deposit covering many orders. Autymate reads those fees from Shopify Payments, posts them against Shopify Payments Clearing and matches the deposit to it, so the bank feed shows one match instead of dozens. What stays in clearing at month end is orders paid but not yet shipped, the unshipped sales the bookkeeper reviews at close anyway.
Here is where the native sync leaves shipping, payouts and refunds to month end, and what posts instead.
| Situation | With ShipStation's native integration | What QuickBooks receives with Autymate |
|---|---|---|
| A buyer pays $7.95 for shipping | The $7.95 is added to the last product line, so it reads as product sales | Its own line on Shipping Income, so shipping charged and shipping costs can be compared |
| A label is bought from the ShipStation balance | Nothing is sent; the top-up reaches QuickBooks as one lump from the bank or card feed | Autymate posts the label's cost against its order |
| The monthly FedEx or UPS bill arrives for labels on your own account | Nothing is sent; the bill is the only record of those labels, expensed in the month it is paid | Autymate records each label's cost as its order ships, and the FedEx or UPS bill is paid against those costs, so each label is expensed once |
| Shopify or Amazon already posts sales to QuickBooks through another app | Both post the same order, so revenue and tax are doubled | Autymate works alongside that app: each store posts through one system, so nothing posts twice |
| Shopify Payments or Amazon pays out net of fees for many orders at once | Each order sits at full value in Undeposited Funds, and no single deposit matches | Sales post to a clearing account per payout source, and Autymate reads each payout's fees from that source, posts them and matches the deposit |
| An order is paid on September 30 and ships on October 2 | One record, which users report is dated by the run that sends it | Autymate posts on the date your accountant picks, order date or ship date |
| A store refunds an order after it shipped | ShipStation no longer receives updates from the store, so the SS record stays at full value | Autymate reads the refund from the store and posts it against the original sale |
| A label is voided and the order shipped again | The order returns to Awaiting Shipment; ShipStation processes each order once, so it is not expected to post again | Duplicate checks run before anything posts, and Autymate reverses the voided label's cost and posts the new label's |
| An Amazon buyer's email is a relay address | A new QuickBooks customer for each relay address, and a display name already in use is not accepted | Marketplace orders post to customers by the rule your accountant picks, such as one per marketplace |
| A new SKU or kit appears on an order | A new non-inventory item, or a second item with an SS prefix when the name is taken | The order is held for review, with the reason, until your team maps the SKU to an existing item |
| Amazon collects and remits the sales tax on an order | Any tax on the order is mapped to the agency for the buyer's state | Autymate keeps marketplace-remitted tax apart from the tax you owe |
| A late ship date falls in a month you have closed | QuickBooks warns about the closed period, or asks for the closing-date password if one is set, and any change after close shows on the Exceptions to Closing Date report | Autymate posts it to the open month your accountant chose, and anything outside the rules waits in review until your team decides |
Autymate checks every ShipStation order and store before anything posts to QuickBooks.
Every store, SKU, kit and shipping charge points at one QuickBooks company, item or account, and your accountant approves that list before the first live order. A SKU added to a store later waits for a mapping instead of becoming a stray non-inventory item.
Before anything posts, Autymate checks each order or daily summary: are all its SKUs mapped, is it from a store this workflow owns, and do its lines add up to the ShipStation order totals? An order that does not pass is held for review on its own, with the SKU, store or total behind the hold named.
A day's run repeated is caught before posting, so each order still becomes one sale in QuickBooks. An order reshipped after a voided label stays one sale, carrying only the new label's cost. A customer already in QuickBooks is linked rather than created again.
Every QuickBooks record carries a reference to its ShipStation orders, by the store's own order number. At month end, a bookkeeper can start from any line on a receipt or an invoice and land on the ShipStation order behind it, and Autymate reconciles each store's day against ShipStation's own totals.
Autymate's team monitors every run. When an order is held on an unmapped SKU, a store outside the workflow or a buyer with no matching customer, your team gets the order number and the reason.
All five routes get shipped orders into QuickBooks; what changes is who decides how shipping and stores post.
| Option | Best fit | What to consider |
|---|---|---|
| ShipStation's native QuickBooks Online integration | U.S. sellers posting one store or a few, where shipping income and label costs can be sorted by hand | A ShipStation QuickBooks sync that sends one sales receipt or invoice per shipped order, with shipping inside product income. U.S. QuickBooks Online only, and no label cost |
| Partner apps ShipStation lists, such as Webgility or Connex | Sellers who want a packaged connector, including QuickBooks Desktop | Each sets its own rules for orders, fees and shipping expense; check how it treats stores another app already posts |
| Zapier | A single step, such as a shipped order creating a QuickBooks invoice | Four ShipStation triggers and no step for label cost, voids or adjustments; mapping and duplicate checks are left to whoever builds the zap |
| A custom build on the ShipStation API | An in-house developer ready to maintain the integration, on the Standard or Premium plan | API access starts at the Standard plan; V1 allows 40 requests a minute, and ShipStation's webhooks do not cover voids, cancellations or edits |
| Autymate | Several stores or brands, a wholesale channel, shipping costs you want tied to orders, or books shared with other systems | Your accountant approves how each store, shipping charge and label posts before go-live, and Autymate's team keeps watch on every run after that |
One U.S. store with few labels can stay native; several stores, channels or brands need more.
You sell through one or two stores into one U.S. QuickBooks Online company, no other app posts those sales, and a few dozen orders a day is your volume. Someone moves shipping income out of product sales by hand when it matters, and shipping costs are booked from the bank or card statement and the FedEx or UPS bill.
Bring in a ShipStation accounting integration from Autymate once you sell on several channels or brands, when a Shopify or marketplace connector also reaches your books, when label costs need to tie back to orders, or when a wholesale store bills on terms.
Where Autymate Fits: your warehouse keeps ShipStation exactly as it runs today, from rate shopping to labels and tracking. Autymate works alongside ShipStation's own sync and any Shopify or Amazon connector: your accountant picks the system that posts each store, so nothing posts twice.
From a review of your stores to the first day of orders posted and watched, in five steps.
We list every store connected to ShipStation, which channels already post sales to QuickBooks through other apps, how you pay for labels, and what ShipStation's native integration sends today. On the QuickBooks side we confirm your item list, income accounts, classes, the closing date, and how many company files your brands need.
Your accountant chooses one record per order, a daily summary per store, or a hybrid. They decide where shipping income, discounts and label costs post, how marketplace tax and refunds are recorded, and which company or class each store belongs to.
We build the mapping from a recent month of your ShipStation orders and label exports, so the SKUs, kits, stores and carriers on them are mapped before a live order posts.
Before go-live we push real cases through: a split order, a voided and reprinted label, an Amazon order with marketplace tax, a new SKU, a free-shipping order and a wholesale invoice. Then we compare QuickBooks with ShipStation's Shipments report, store by store and day by day.
From go-live, each day's shipped orders follow the ShipStation to QuickBooks Online rules your accountant approved. If an order fits none of them, it waits in review and Autymate support resolves it alongside your team.
Your QuickBooks after one month of ShipStation QuickBooks automation: shipping, label costs and stores each readable.
Shipping charged sits on its own account, so the profit and loss report shows what buyers paid for shipping against what the labels cost.
Retail stores post daily summaries and the wholesale store posts invoices on terms, side by side in the same QuickBooks file.
Your ShipStation stores share their accounts and classes with payroll, payments and anything else posting to QuickBooks through Autymate's 300+ other connections.
Yes, you can integrate ShipStation with QuickBooks Online using Autymate.
ShipStation also has its own integration for U.S. QuickBooks Online accounts, listed on all of its current plans, which suits one or two stores posting an order at a time. A ShipStation QuickBooks Online integration from Autymate suits sellers running several stores, brands or QuickBooks companies, or a wholesale channel on terms, and leaves ShipStation exactly as the warehouse uses it.
To connect natively, go to Settings, Integrations, Integration Partners in ShipStation, choose QuickBooks Online and authorize it.
You then pick sales receipts or invoices, the accounts they post to, which stores send, whether customers are exported and how tax agencies map by state. With Autymate, the ShipStation to QuickBooks Online connection runs on ShipStation's API, included from the Standard plan, and is built for your stores and proven on a month of orders you have already shipped.
Either, but one type for every store.
ShipStation QuickBooks sales receipts post to the asset account you choose, such as Undeposited Funds (shown as Payments to deposit in some companies), which suits orders paid at checkout. Invoices post to Accounts Receivable, which suits wholesale on terms. With Autymate, retail stores post sales receipts or daily summaries while a wholesale store posts invoices, in the same QuickBooks company.
ShipStation's field mapping adds Shipping Paid to the amount on the last product line of the sales receipt or invoice, so it is counted as income from that product.
There is no separate shipping line. With Autymate, shipping charged posts to its own Shipping Income account, so it can be compared with what the labels cost.
The native integration does not send label cost, so shipping cost reaches QuickBooks only as balance top-ups in the bank or card feed, or as the FedEx or UPS bill.
Treat top-ups as prepaid postage, expense each label as it is used, and post carrier adjustments and their processing fees to their own account. With Autymate, each label's cost comes from ShipStation's API and posts against its order, so the top-ups and bills clear what is already recorded.
When a Shopify, Amazon or other channel connector posts sales to QuickBooks and ShipStation's integration sends the same store's orders, each sale is recorded twice, with its tax.
ShipStation lets you choose which stores send, so leave out any store whose channel already posts. Autymate works alongside those connectors: your accountant picks the one system that posts each store, before the first order posts, so nothing posts twice.
Not through ShipStation, which does not hold the buyer's payment and so has no processing or marketplace fees to send.
Shopify Payments, Amazon and PayPal each pay you with their fees already taken out, and one deposit usually covers many orders. Autymate gives each channel its own clearing account for sales, reads each payout's fees from that channel, posts them there and matches the deposit to what is left.
Not natively: ShipStation's QuickBooks sync creates one sales receipt or invoice per shipped order.
With Autymate, it can: your accountant picks one sales receipt per store per day, which keeps the deposit screen and the customer list short, and wholesale orders still post one invoice each.
ShipStation processes each order once and stops receiving store updates after an order ships, so a refund made in Shopify or Amazon later does not change the sales receipt.
A voided label moves the order back to Awaiting Shipment, and a ShipStation Carriers label's cost returns to the balance, most the same day and some up to 21 business days later. Autymate reads the refund from the store and the void from ShipStation, and posts each against the original record.
Yes, with Autymate.
ShipStation's help describes connecting one QuickBooks Online account and sending the stores you choose to the accounts you set. With a ShipStation QuickBooks integration from Autymate, the store an order came from picks its QuickBooks company, so a brand that is its own LLC keeps its own books, while stores under one company post as classes or locations.
No.
ShipStation's help center says its QuickBooks integration is only for U.S.-based QuickBooks Online accounts, so QuickBooks Online Canada and other countries fall outside it, and it does not send GST/HST. For other QuickBooks versions it points to Connex. Autymate supports QuickBooks Desktop too, so a seller whose books stay on Desktop has its ShipStation orders posted to that file.
ShipStation numbers each record SS plus its order ID, and its manual run picks orders by order date or ship date.
Users in ShipStation's community have reported receipts dated on the day they were sent rather than the ship date, and invoice numbers that differ from their own order numbers. With Autymate, every record carries the store's order number and the posting date your accountant picks.
Send us a month of shipped orders and label exports, plus the stores, brands and QuickBooks companies involved. We map their SKUs, shipping charges and label costs to your accounts, then show you how to connect ShipStation to QuickBooks with those rules in place for your next order.
Intuit Gold Partner
SOC 2 Type II
1,000+ Five-Star Reviews