Overview

In a few simple steps, you will be able to sync your invoices between Bonsai and QuickBooks Online. This means you won't need to manually upload invoices and your information will always be in sync between your two accounts.

Note: To confirm if your paid subscription has access to this integration, visit our pricing page.

What information is synced between Bonsai and QuickBooks Online?

When you sync an invoice from Bonsai to QuickBooks Online, the following invoice data will be pushed:

Client / Company name
Client / Company address
Invoice number
Invoice / Issued date
Invoice / Due date
Invoice / Item name
Invoice / Discount (if applicable)
Invoice / Tax amount (if applicable)
Invoice / Expenses (will be pushed as line items)
Payment date and amount (when invoice is paid)

Note: at this time, the QuickBooks Online integration only syncs invoice amounts without online payment fees.

Connecting to QuickBooks

If you're new to using the QuickBooks Online integration:

Navigate to the profile icon in the bottom lefthand corner of your account
Select 'Settings'
Select 'Integrations & Data'

Here, you can select the QuickBooks Online integration:

Next, select your preferences for when invoices are synchronized between Bonsai and QuickBooks Online:

Once you're ready, select 'Connect to QuickBooks'.

This will redirect you to a QuickBooks Online login screen where you can sign into your QuickBooks account:

Once you've signed into your QuickBooks Online account, you'll be redirected to the Bonsai integration page where you'll see a checkmark that indicates QuickBooks Online is now connected:

Once you're connected, when you navigate to your Invoices page, you'll notice a syncing icon to the right of each of your invoice lines. Each time an invoice has successfully synced to QuickBooks Online and the icon will turn green:

If you've previously connected to the QuickBooks Online integration:

All you need to do to update your QuickBooks Online integration to the latest version is disconnect and then reconnect. This will not impact any of the data previously synced between Bonsai and QuickBooks Online. Follow these steps to disconnect your current QuickBooks Online integration:

Navigate to the profile icon in the bottom lefthand corner of your account
Select 'Settings'
Select 'Integrations & Data'

Here you can select the QuickBooks Online integration:

Next, select 'Disconnect':

Once you've disconnected from QuickBooks Online, you'll receive a message in the bottom righthand corner that says "Successfully disconnected from QuickBooks":

With that, you'll notice that the QuickBooks Online integration no longer has a checkmark next to it to indicate a connection:

When you're ready, select 'QuickBooks Online' to reconnect to the integration.

Here, you can choose your new integration preferences and select 'Connect to QuickBooks':

Once completed, this will ensure that you're connected to the latest version:

Now you're ready to start syncing your invoice data to QuickBooks Online.

Sync Settings

How invoice syncing works

Bonsai can sync invoices to QuickBooks Online both when an invoice is first created in QuickBooks and when an already-synced invoice is subsequently updated in Bonsai.

Please note: An invoice may be pushed to QuickBooks more than once. When an already-synced invoice is sent from Bonsai, marked as paid in Bonsai, or paid through Bonsai (including card, ACH, or PayPal payments), Bonsai pushes the invoice to QuickBooks again.

During each subsequent sync, Bonsai re-applies your Services Mapping settings to the invoice line items. This means any manual changes you've made to the Product/Service fields directly in QuickBooks Online may be overwritten.

Disabling the automatic push settings only prevents the initial automatic sync of Sent or Paid invoices. It does not prevent subsequent updates to invoices that have already been synced.

If you want to make manual changes to an invoice's Product/Service fields in QuickBooks, we recommend doing so only after the invoice has been sent from Bonsai. To preserve those changes, record subsequent payments directly in QuickBooks Online rather than Bonsai.

Manual Syncing

You have the ability to manually sync 'drafted' invoices or invoices that you created prior to connecting to the integration. To manually sync an invoice, simply navigate to Financial Management > Invoices.

Here you can manually select the syncing icon on the righthand side of your invoice:

Once you've selected this, this will push your invoice into QuickBooks Online:

This way, you can stay up-to-date with any invoice or invoice drafts you have across Bonsai and QuickBooks Online.

Automatic Syncing of Paid Invoices:

You have the ability to automatically sync invoices that have been paid from Bonsai to QuickBooks Online.

To set your preferences to allow this:

Navigate to the profile icon in the bottom lefthand corner of your account
Select 'Settings'
Navigate to 'Integrations & Data'
Select 'QuickBooks Online'

Here, select 'Automatically push Paid invoices from Bonsai to QuickBooks':

Next, select 'Connect to QuickBooks'.

This will ensure that all paid invoices moving forward will sync to QuickBooks Online.

Note: These settings control the initial automatic sync of invoices to QuickBooks Online. They do not prevent subsequent pushes when an already-synced invoice is sent, marked as paid, or paid through Bonsai. During subsequent pushes, Bonsai re-applies your Services Mapping to the invoice line items, which may overwrite manual Product/Service changes made directly in QuickBooks Online.

Automatic Syncing of Sent Invoices:

You have the ability to automatically sync invoices that have been 'sent' to your clients, but have not yet been paid.

When you are connecting to the QuickBooks Online integration, select 'Automatically push Sent invoices from Bonsai to QuickBooks':

When you're ready, select 'Connect to QuickBooks'.

This ensures that any invoice that you've 'sent' to a client in Bonsai, is automatically synced within QuickBooks Online. This allows you to track the progress of your invoices every step of the way.

Syncing data from QuickBooks Online to Bonsai

To preserve manual changes made directly in QuickBooks, we recommend recording payments in QuickBooks rather than marking invoices as paid or collecting payments through Bonsai.

Our QuickBooks Online integration can retrieve data from QuickBooks and sync it to your Bonsai account. This means that when you receive an online payment or record a payment on an invoice in QuickBooks, you can sync that paid status within Bonsai.

Important: Payment status syncing does not trigger another invoice push.

When an invoice payment is recorded directly in QuickBooks Online, Bonsai receives the updated payment status and marks the corresponding invoice as paid.

This update only syncs the payment status from QuickBooks to Bonsai. It does not push the invoice back to QuickBooks or overwrite any manual changes made to its Product/Service fields.

To preserve manual changes made directly in QuickBooks, we recommend recording payments in QuickBooks rather than marking invoices as paid or collecting payments through Bonsai.

When you are connecting to the QuickBooks Online integration, you'll want to select 'Automatically sync Paid invoices from QuickBooks to Bonsai':

Once completed, you'll have the ability to sync a paid invoice status from QuickBooks Online into Bonsai.

To action syncing a paid invoice from QuickBooks Online to Bonsai, you must receive an online payment in QuickBooks or manually record a payment in QuickBooks.

To manually record a payment in QuickBooks Online:

Sync your 'drafted' or 'sent' invoice from Bonsai to QuickBooks Online:
From here, in QuickBooks Online, select 'receive payment' to record the payment:
Once you've recorded payment in QuickBooks Online, it will update the synced invoice status in Bonsai from ‘drafted’, ‘outstanding’, ‘overdue’ to ‘Paid’:

Map line items between your Bonsai and QuickBooks Online invoices

How services mapping works

You can map your Bonsai services to specific QuickBooks Online items to ensure invoice line items are categorized correctly in QuickBooks.

You can also set a default QuickBooks Online item to be used when a Bonsai invoice line doesn't match any of your configured service mappings.

Important: Services Mapping uses exact name matching.

When syncing an invoice, Bonsai compares each invoice line item's name against the names of your services in Bonsai. The match must be exact, including spelling and capitalization.

If the invoice line item's name exactly matches a Bonsai service name, the corresponding mapped QuickBooks item will be used.
If the line item doesn't match an existing Bonsai service name, Bonsai will use your default QuickBooks Online item.
If a mapped QuickBooks item becomes inactive, Bonsai will fall back to the default item.

To ensure the correct mapping is applied:

When adding an invoice line item, select the appropriate service from your Bonsai services list rather than manually typing a different name.
Keep the service name as the line item name.
Add specific details, such as vendor names, campaign names, or project information, in the description field.

For example, you can use "Sales Media" as the line item name and "Powtech campaign" as its description.

Since Bonsai sends both the item name and description to QuickBooks, the line will appear as "Sales Media - Powtech campaign."

Additional notes:

Selecting a service automatically populates its default description and rate. You can edit these after selecting the service.
If you're creating invoice lines from time entries, the services list isn't available. In this case, manually enter the exact Bonsai service name as the line item name to ensure the mapping works correctly.
Bonsai does not automatically create new services or item codes in QuickBooks Online.

Or set a default QuickBooks Online item for all your Bonsai invoice line items:

If a mapped QuickBooks item becomes inactive, Bonsai will fall back to the default item.

Keep in mind that all existing invoice sync preferences and tax rate mappings remain unchanged.

What happens when an already-synced invoice is updated?

Once an invoice has been synced to QuickBooks Online, Bonsai continues to keep the invoice updated when certain actions occur in Bonsai.

For invoices that have already been synced, the following actions trigger another push to QuickBooks Online:

Sending the invoice from Bonsai.
Marking the invoice as paid in Bonsai.
Receiving a payment through Bonsai, including card, ACH, or PayPal payments.

When this happens, Bonsai sends the invoice again and re-evaluates each line item's Product/Service using your configured Services Mapping.

What does this mean for manual changes in QuickBooks?

If you manually change a line item's Product/Service in QuickBooks Online after the initial sync, a subsequent push from Bonsai may overwrite that change and restore the item selected by your Services Mapping.

For this reason, we recommend making any manual Product/Service adjustments in QuickBooks only after the invoice has been sent from Bonsai.

If you need to preserve those manual changes, record subsequent payments directly in QuickBooks Online. These payment updates sync back to Bonsai without triggering another push of the invoice.

Already made manual changes that were overwritten?

If a subsequent sync has overwritten your manual QuickBooks changes, you'll need to correct the Product/Service fields directly in QuickBooks again. Bonsai does not retain manually selected Product/Service values from QuickBooks and cannot automatically restore them.

Detailed data syncing rules

1. Client Information:

If the client does not have a Bonsai account, the company name or default contact name is sent.
If the client has a Bonsai account, the company name is sent.

2. Address and Email:

The client’s profile address and email are sent if they have a Bonsai account. This data is only passed to QuickBooks Online when the client is created.

3. Invoice Line Items:

Line items with descriptions are sent as “Name - Description.” If no description is available, only “Name” is sent.
New services or item codes are not created in QuickBooks Online.

4. Invoice Amount with Online Payment Fees:

The original invoice amount is sent, excluding payment fees.
Example: For a $100 invoice with $3 in fees, $100 is sent.

5. Expenses:

Currently, expenses are sent as invoice line items with the format: "Expense — Name of the expense."

6. Tax:

0% Tax Rate: Works without additional setup for US users.
Non-0% Tax Rate: You must ensure the corresponding custom sales tax rate is created in QuickBooks Online. Helpful article: Custom Rates in QuickBooks Online

7. Discounts:

Discount amount is pushed to QuickBooks Online

Note: Discrepancies may occur in invoices with discounts, tax > 0%, and expenses due to different discount application methods between Bonsai and QuickBooks.

- In Bonsai the full discount amount is applied to the subtotal excluding expenses.
- In QuickBooks the discount is pro-rated within line items from both the taxable subtotal and the non-taxable subtotal. As Expenses are passed as non-taxable line items, QuickBooks is prorating part of the discount to those expenses, which creates a difference between the taxable subtotal in Bonsai and QuickBooks.

8. Tips:

Tips are not supported by the integration.

How To Find A QuickBooks Online Customer ID

When syncing Bonsai invoices to QuickBooks Online, you can choose exactly which customer they belong to by entering that customer’s unique QuickBooks Online ID.

Here’s how to find it:

Step 1: Go to the Customers list in QuickBooks

In QuickBooks Online, go to the Customers section

Step 2: Open the customer’s profile

Click on the customer you want to map to a Bonsai client.

Step 3: Check the URL

QuickBooks includes the customer ID in the URL of the customer details page.

Example:

The number after ?nameId= (in this example: 39) is the Customer ID.

Step 4: Add it to Bonsai

Copy this number into the QuickBooks Online ID field in your Bonsai client profile:

Once saved, Bonsai will sync invoices to that exact customer—no duplicates, no mismatches.

Integration Limitations

Partially paid invoices are not synced.
Online payment fees and refunds are not sent to QuickBooks Online.
Invoices that have been synced to QuickBooks Online and later deleted cannot be re-synced.
Non-invoice income is not sent to QuickBooks Online.