There are three ways to set up a FreshBooks and QuickBooks integration. Intuit's guides show a FreshBooks connector, built by OneSaas, that sends FreshBooks invoices, payments and expenses to QuickBooks Online every hour. Check it still shows under Apps first, because Intuit moved Shopify stores off the same connector in 2026. A Zapier zap can make a QuickBooks invoice, payment or expense for each new one in FreshBooks. Or you export CSV files from FreshBooks and import them into QuickBooks. Where they stop: each tax, product and payment type has to be mapped by hand, QuickBooks can't import discounts or credit memos from a file, and nothing checks that the two sets of numbers still agree. AI agents do that check.
Why people look for a FreshBooks and QuickBooks integration
It usually comes up in one of two ways. A business sends its invoices and tracks time in FreshBooks, but its accountant keeps the books in QuickBooks Online. Or the business has grown and wants to move to QuickBooks without losing its history.
Either way, connected has to mean the same thing in both places: each invoice, payment, credit and expense shows once, with the right customer, the right tax and the right account. Moving the invoices across is the easy part. Making sure the totals in both programs still match a month later is the part that takes hours.
Three ways to connect FreshBooks to QuickBooks
Which one fits depends on whether you keep both programs or move off FreshBooks.
Intuit's FreshBooks connector
- How it works
- Intuit's community guides from 2021 show a FreshBooks connector under Apps in QuickBooks Online. It runs through QuickBooks Connector, made by OneSaas, which is now part of Intuit. You connect FreshBooks, then set which invoice statuses come across, whether they arrive as invoices or sales receipts, how products and taxes match, and whether payments and expenses come too. It can sync every hour.
- Good for
- Businesses that keep invoicing in FreshBooks and want the books in QuickBooks without typing.
- Where it breaks
- Each FreshBooks tax has to be matched to a QuickBooks tax code, and products are matched by SKU. Invoices dated before the start date never come across. In 2026 Intuit moved Shopify stores off QuickBooks Connector to a new app, so check that the FreshBooks connector still shows under Apps before you plan around it.
A Zapier zap
- How it works
- Zapier's FreshBooks triggers include New Invoice, New Invoice Payment, New Expense and New Credit Note. Its QuickBooks Online actions include Create Invoice, Create Payment, Create Expense and Create Credit Memo.
- Good for
- Small firms with simple invoices, one tax rate and a few clients.
- Where it breaks
- Each case is a zap you build: invoices, payments, credits, expenses and edits. An invoice changed in FreshBooks after it went across stays as it was in QuickBooks unless you build a zap for updates too. A zap that fails doesn't tell your bookkeeper.
Export from FreshBooks, import into QuickBooks
- How it works
- FreshBooks exports clients, invoices, expenses, items and reports as CSV files. In QuickBooks Online, Settings, then Import data, takes customers and invoices from a file.
- Good for
- A one-time move from FreshBooks to QuickBooks.
- Where it breaks
- QuickBooks imports up to 100 invoices at a time, 1,000 rows per file, and can't add discounts or credit memos that way. Estimates and proposals only come out of FreshBooks as a CSV if you ask its support team.
Arkeo agents
- How it works
- Agents read new invoices, payments and expenses in FreshBooks each day, check what reached QuickBooks, and list what is missing, doubled or on the wrong customer. They also chase the unpaid invoices and file the receipts.
- Good for
- Firms that bill from FreshBooks, keep the books in QuickBooks, and need both to agree at month end.
- Where it breaks
- Anything your rules keep for a person, like a write-off or a credit to a client, goes to your team in one message.
How to connect FreshBooks to QuickBooks Online: five steps
These follow Intuit's guides for the FreshBooks connector and its import pages. Open them for the screens.
- 1Plan your accounts and taxes first
Ask your bookkeeper which QuickBooks accounts, tax codes and products each FreshBooks invoice line should land on, and whether payments go to a clearing account.
- 2Add the FreshBooks connector
In QuickBooks Online, go to Apps and look for the FreshBooks connector. If it's listed, select Connect. On the Connections tab, select Connect to FreshBooks, sign in, and select your FreshBooks business.
- 3Set what comes across
Select Manage. Set which invoice statuses sync, invoices or sales receipts, the start date, product matching, tax codes, payments and expenses. Then turn on the hourly sync.
- 4Or move the history with files
In FreshBooks, export clients, invoices and expenses as CSV files. In QuickBooks, go to Settings, then Import data, then Invoices, map the columns and select Start import.
- 5
Check one month by hand
Run the invoice and payment totals for one month in both programs and compare them line by line. Then do it again each month.
What still has to be done by hand
Keeping both programs means keeping two sets of numbers that have to agree. Intuit's own guide for the connector is a list of choices someone has to get right: which FreshBooks statuses count, invoices or sales receipts, a QuickBooks tax code for each FreshBooks tax, a product match by SKU, and accounts for each payment type. It tells you to ask your accountant. Invoices dated before your start date never come across, so the first months often have to be entered another way.
Files don't fill the gap. QuickBooks takes 100 invoices at a time and can't import discounts or credit memos from a file, so those are typed in. FreshBooks only sends estimates and proposals as a CSV by request to its support team.
People have hit this for years. In an Intuit Community thread from 2018 to 2020 on moving from FreshBooks to QuickBooks Online, the answers pointed to connector apps and other tools, and one member said the tool they were offered could move everything except invoices, the one thing they needed.
And the connector itself may change. A MyWorks support page says Intuit retired QuickBooks Connector for Shopify stores in 2026 and moved them to a new app. Nothing tells your bookkeeper when an hourly sync stops, so someone has to check.
The agents that do it
Each agent does one job from start to finish in your own FreshBooks, and passes what the books need to QuickBooks.
No more lost hours at month end.
- Flags missing timeevery Friday
- Adds up billable hours per clientper billing period
- Builds the invoicesame day
Get paid without chasing clients yourself.
- Checks unpaid invoicesevery morning
- Sends the client a friendly reminderon your schedule
- Tells the owner about anything over 30 daysevery Monday
Client expenses get billed, not lost.
- Reads receipts from your inboxas they land
- Adds the expense to the right client and projectsame day
- Flags spending with no receiptevery week
Questions
Is my customers' information safe?
Yes. Agents work in your own FreshBooks and QuickBooks and see only what their job needs. Customer details never go into public AI. Agents connect to AI through business-grade connections audited under SOC 2.
Does FreshBooks integrate with QuickBooks?
Not from inside FreshBooks. The connections come from Intuit's FreshBooks connector in QuickBooks Online, from Zapier, or from exporting FreshBooks files and importing them into QuickBooks.
Can I move all my FreshBooks data to QuickBooks?
Clients, invoices, expenses and items export from FreshBooks as CSV files, and QuickBooks imports customers and invoices. Discounts and credit memos can't come in from a file, and estimates need a request to FreshBooks support.
Will this replace my bookkeeper?
No. Your bookkeeper sets the rules and reviews the books. Agents do the moving and the checking, so your bookkeeper's hours go to the work that needs them.
What does it cost?
You get the price on the call, along with the hours it saves your team.
Sources
- quickbooks.intuit.com: freshbooks and quickbooks online integration guide 284759
- quickbooks.intuit.com: connect freshbooks cloud accounting to quickbooks online 284761
- quickbooks.intuit.com
- support.freshbooks.com
- zapier.com: quickbooks
- quickbooks.intuit.com: how do i transfer from freshbooks to quickbooks online 69392
- support.myworks.software: migrating from onesaas quickbooks connector to myworks sync