Integrating with QuickBooks Online

Our QuickBooks Online integration allows you to sync transaction details and automatically create accounting records in QuickBooks by assigning GL (General Ledger) codes to transactions directly from your Mercury dashboard.

Connecting to QuickBooks

1. Click your company name in the top left-hand corner of the dashboard
2. Go to Settings > Integrations
3. Hover over QuickBooks and click Connect
4. Follow the instructions to connect Mercury to your QuickBooks bank feed
5. Optional: Set up Enrichment to enable the auto-categorization of your transactions and sync additional transaction fields to your accounting records
   • Follow the prompts to connect to QuickBooks and map your Mercury accounts to QuickBooks general ledger accounts to ensure proper syncing
   • Click Complete
     • Note: Enriching your QuickBooks integration is only available for QBO SimpleStart and higher plans. The QBO Solopreneur plan is not supported at this time

After connecting

• Once connected, QuickBooks will show as "Active" on your Integrations page, where you can manage and check the status of the connection at any time
• If you don’t see the option to add GL codes or an account is missing:
  1. Ensure your QuickBooks bank feed is connected
  2. Set up Enrichment to:
     • Let Mercury automatically categorize your transactions 
     • Sync accounting records with QuickBooks
     • Enrich your QuickBooks sync with GL codes, attachments, notes, and memos

Disconnecting from QuickBooks

To disconnect your QuickBooks integration, you'll need to remove the connection in both Mercury and QuickBooks.

1. Go to Settings > Integrations in Mercury on web
2. Click Disconnect next to QuickBooks
3. Open QuickBooks and confirm the bank feed is also disconnected via Bank Transactions > Link Account > Manage Connections
    

Applying QuickBooks GL codes

Once you connect to QuickBooks and set up enrichment, Mercury will automatically pull in your QuickBooks GL codes so you can add them to transactions and create and sync the associated accounting records to QuickBooks.

Whenever possible, Mercury will use AI and your categorization history to pre-fill GL codes for your transactions - these suggestions will be indicated with a sparkle icon. You can always overwrite them by clicking on the dropdown and selecting a new input. The suggested GL codes will improve over time, the more you interact with the feature.

You can also manually apply GL codes to transactions in a few different places: 

• On your Accounting page, select individual or multiple transactions and pick a GL code from the dropdown
• On your Transactions page, click open a Transaction to view the details and select from the GL code dropdown
• If you’re creating a new payment manually or by uploading an invoice, you'll have the option to select GL codes
• If you want to add a category to an upcoming payment that was already scheduled, you can view the payment details on your Payments page and select from the GL code dropdown there

Syncing transactions to QuickBooks

1. On the Accounting page, review your transactions and ensure all required fields (eg. GL code, counterparty, etc) are filled in
2. Select individual or multiple transactions and click on the Mark as Ready action 
3. You can then push any ready transactions to QuickBooks by clicking the Sync button
   • This action brings any additional transaction attributes (GL codes, classes, counterparty, attachments, and/or notes) you've added in Mercury to your accounting software, and matches them to the original transaction record there

Accounting record details

The type of accounting record created, the timing of the sync, and the data included will vary with each transaction type.

FAQs 

Is the integration with QuickBooks free to use?

Yes. Our QuickBooks integration is free to use. Learn more about pricing.

Why did my bank feed connection stop working, and how do I fix it?

You'll need to reset the connection on both sides — in Mercury and in QuickBooks. Here's how: 

1. Disconnect the bank feed in Mercury via Integrations
2. In QuickBooks, go to Bank Transactions→ click the Link Account dropdown → select Manage Connections
3. Find all Mercury connections and un-toggle each account listed under them
   • This step is key to ensuring a healthy reconnection 
4. Re-establish the bank feed connection from Mercury using the steps listed here

What types of transactions can have GL codes applied to them?

You can categorize incoming and outgoing wires, ACH transfers, and checks. The only transaction types currently excluded are internal transfers and IO payments.

Why can’t I categorize transfers and IO payments?

Transfers and IO payments are categorized automatically by our system and/or QuickBooks. 

Can I turn off enriched categorization for my QuickBooks integration?

No — you can’t turn off enriched categorization after your integration is set up.

If you’d prefer not to use it, you have two options:

• Ignore enriched categorization:
  You can leave categorization fields in Mercury untouched and manage everything directly in QuickBooks. Your transactions will still sync via the bank feed. Additional data (like categories or notes) is only sent if you take action in Mercury, though some transactions (like internal transfers) may still be automatically categorized and synced.
• Reconnect with bank feed only:
  You can disconnect and reconnect your QuickBooks integration, and during setup choose to connect only the bank feed (skipping enriched categorization).

Enriched categorization is optional, but allows you to add categories, notes, and attachments in Mercury and sync that information to QuickBooks alongside your transactions.

Do you support Treasury transactions in the bank feed? 

Yes. For QuickBooks, navigate to Transactions > Bank transactions, then click “Link account” button (not the arrow next to it) and go through the steps to authenticate. Locate your Treasury account from the list, map it to a Quickbooks GL, and click Connect. 

Some important things to note: 

• After clicking “Link account,” you may be able to select a saved Mercury connection or create a new one: we suggest creating a new one. You can locate “Mercury” under “Recommended” at the bottom of the page, or search for “Mercury” in the search bar.
• If you had a Mercury Treasury account linked to QuickBooks before April 2025, we recommend the below steps to reduce transaction duplication:
  • Map your account to the same GL code you used for Treasury before
  • In the “Link account” flow, select a start date (at the bottom of the page) that is after the last Treasury transactions register date in QuickBooks

If I create a recurring payment, will the same GL code be assigned automatically to all future payments?

Yes, the GL code you assign to the first payment will be automatically assigned to all future payments in the series.

If I make changes in QuickBooks to a transaction, will those changes be reflected in my Mercury account?

No, the connection is a one-way sync. Transaction information is passed from Mercury to QuickBooks, and any changes in QuickBooks won’t pass back to Mercury.

What QuickBooks plans does this integration work with?

Categorizing and syncing payments is only available for the QuickBooks Online Essentials tier or higher. We also don’t currently support QuickBooks Desktop. Learn more about QuickBooks plan options.