QuickBooks Integration: How It Works

It’s safe to say no one wants to spend hours copy‑and‑pasting information into QuickBooks — which is exactly why this integration exists.

The video below quickly explains the integration settings. The rest of this article covers how to purchase and activate the integration.

Before anything else, make sure your Goodshuffle Pro and QuickBooks Online accounts are connected through your Integrations.
If you haven’t done this yet, check out our guide:
👉 How can I connect with QuickBooks Online?

It's very important to note that when you activate the QuickBooks Online integration *dramatic pause* nothing will happen (well, your card on file will be charged the additional monthly fee, but that's it - promise).

We won't automatically randomize, edit, and delete any of your existing invoices, and we won't change all of your Customers' names to "Bevo".  

Now that we've got that out of the way, here's what you will see....

The first thing you'll notice is that the QuickBooks Online section now looks like this:

Once connected, click Import Contacts to pull your existing QuickBooks Online customers and related businesses into Goodshuffle Pro.

After the integration is active, any new person or business added to a synced project will push details to QuickBooks Online and update the corresponding Customer record there.

With the integration active, any time a person or business is added to a project that is synced with QuickBooks Online, those details will be pushed to QuickBooks Online and update the Customer record there as well.  Going forward, all contact changes should be made primarily through Goodshuffle Pro.

Clicking Activate will not automatically sync your old projects — it only applies to future projects.

After syncing, you'll see a "Synced" date next to the "Sync" button.

Goodshuffle Pro automatically keeps the invoice updated based on contract changes, and you can click “Resync” at any time.

Within the integration settings, you can:

Any projects/payments created before activating the integration will not auto-sync.

They default to Do Not Sync to avoid duplicate data if you've manually reconciled in QuickBooks Online.

To sync them:

If the client isn’t already in QuickBooks Online, Goodshuffle Pro will:

⚠️ Changing a client on a project affects the linked invoice and payment. Learn more here.

Invoice content:

When you view a synced Goodshuffle Pro invoice in QuickBooks Online, you'll see that we've unpacked all of the line items into the Invoice.

Your Services, Product Rentals, and Product Sales will be broken out on your Chart of Accounts.

You can customize how these revenue accounts are broken out in QuickBooks Online. Note that the image above shows revenue accounts broken out by item sub-category.

Learn how to change the revenue accounts used in QuickBooks Online here.

These tax types (and Overridden taxes) will be broken out on your Chart of Accounts.

If you've set a contract-level "Additional Discount", it will be reflected in the subtotals section of the Invoice, along with a summary of any payments that may have been captured.

Finally, we automatically attach a copy of the signed contract because, well, we love your accountant and we're sure this will make their (or your!) life easier.

I'm glad you asked. You may have noticed in the top right corner of the Invoice that a payment has already been applied to it.

If you click the blue "1 Payment" text, you'll get taken to a screen in QuickBooks Online that looks like the image below, showing the details of the Payment that Goodshuffle Pro created when the Credit Card/ACH charge was synced:

Payments automatically:

Refunds appear as:

Goodshuffle Pro pushes online refunds to QuickBooks Online and generates an Expense linked to an Accounts Receivable Account that looks a little something like this:

Similar to the Payments, this refund has been linked to the QuickBooks Online Customer, with the proper date, payment method, and amount set. 

Also, attributing the Expense to Accounts Receivable allows us to reduce the amount of the original payment that is applied to the Invoice. For example, you'll see this charge for $1000 that was refunded a couple of times. As a result, only $700 of the original payment is, and should be, applied to the Invoice.

You may have noticed that both the Payments and Expenses (aka Refunds) were being "Deposited to" and "Refunded From" the Undeposited Funds Account, and there's a very good reason for that, which is covered in the next section.

Offline refunds (e.g., paper checks):

The screenshot below is an example of a vendor writing a $25 check to refund a credit card charge that was processed through Goodshuffle Pro.

Goodshuffle creates:

This allows you or your accountant to quickly report on and view a listing of all transfers originating from Goodshuffle Pro. The Account will look like this in your Chart of Accounts.

A single transfer in that account will look like this:

If you click on that entry and click "Edit" you'll see the details of the transfer.

Each deposit includes:

We're able to link those Payments and Expenses to this Bank Deposit because we attributed them to the Undeposited Funds account.

To learn more about Batch transfers and why multiple charges and refunds from
different projects are included in the same transfer, check out this article.

If legally allowed in your area:

This line item is implemented as a Service, connected to an account in your Chart of Accounts called Merchant Fees (Expense/Bank Charges).  

Any refunds against charges where processing fees were passed on will be reflected as Expenses, showing the gross amount refunded (e.g., the number you typed in plus the refundable processing fees).  For a refund, you'll notice the line item for net processing fees will be reduced.

It's important to note that these Merchant Fees are purely to track the total dollar amount that you charged the client and should not be confused with the Payment Processing Fees related to Bank Deposits that reflect the net processing fees for all of the charges and refunds grouped within that particular Bank Deposit.

Just like projects, Charges, Refunds, and Transfers have their own sync/resync buttons.

Click the “+” icon to view and manage these individually.

Example

Let's say you've just created an invoice in Goodshuffle Pro.

This will create an event on your A/R Register.

Looking into more detail will reveal that the invoice has created a Debit on your A/R Account.

When your client pays, the amount in your A/R Register will be reduced.

Any payments will also be recorded in the A/R Aging Report.

Here is a screenshot with more details on the payments for that customer on that report.

Diving deeper into when a client pays reveals that it will Debit Undeposited Funds (increasing the amount in Undeposited Funds) and Credit A/R (reduce the amount in A/R).

Finally, with a transfer, you will see a Debit to your bank account (increasing the amount in your bank), a Debit to the Payment Processing Fees Account (increasing the Processing Fees Expense Account), and Crediting the Undeposited Funds Account (reducing the amount in the Undeposited Funds Account).

👉 Want to see how this works with a non-US account? Click here.

Review this article and contact our support team if you need help.

Yes! You can update sync triggers (e.g., by Logistics Start or Signature Date) in the Integrations Tab.

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