How to Sync Clover Transactions with QuickBooks Online Using PayTraQer

October 17, 2025

To download and sync Clover transactions into QuickBooks Online, you must link your Clover account with PayTraQer. This article explains how to integrate your Clover account with PayTraQer.

Video Tutorial for How to Connect and Sync Clover Transactions to QuickBooks Online using PayTraQer:

Step 1: Open the Clover connector in PayTraQer

● Log in to PayTraQer with the QuickBooks Online company you wish to sync with Clover.

● In the left menu, select Connectors.

● Choose Payment Connectors to see the payment platforms linked to your PayTraQer account.

Connect the Clover through Connectors.png

● Find your Clover connection in the list before proceeding to the next step.

Step 2: Review how Clover transactions will be recorded in QuickBooks

● In the Clover connector row, click on See How It Works.

Clover - See it works.png

● A User Guide window will open, showing how PayTraQer syncs Clover transactions into QuickBooks entries.

● Under Transaction Recording, check the mapping displayed for your Clover sync.

● Make sure that Payment is recorded as Invoice Payment, and Fees as Expense in QuickBooks.

● Confirm that Customer Refund is listed as Refund in QuickBooks.

Payment System for Clover QuickBooks.png

Payment System

QuickBooks

Payment

Invoice Payment,  Fees as Expense

Customer Refund

Refund

● Click “OK” once you have reviewed the transaction flow.

Step 3: Open the Transactions page in PayTraQer

● On the left menu, select Transactions.

● The Transactions dashboard has various organizational views that assist in managing and checking your data flow:

Section

Purpose

Review

Lists transactions that are ready for syncing.

Synced

Includes transactions that have already been sent to QuickBooks.

Error

List transactions that failed and require correction.

Ignore

Keeps track of transactions you deliberately avoided.

Sync History

Provides a full timeline log of previous syncs.

● Stay in the Review tab to view Clover transactions that are prepared to sync with QuickBooks Online.

Clover Transactions in Review Tab.png

● In the Review tab, click on Filter.

● You can use options such as Date, Amount, Payment System, Transaction Type, Transaction Id, and Contact to filter the records.

● Select Current Page if you want to choose all transactions that are currently displayed.

Filter for Clover.png

● By applying the required filters, you can quickly find the Clover transactions you need to review or sync.

● This makes it easier to work with only the relevant transactions instead of going through each record manually.

● Once you have applied the necessary filters, choose the Clover transactions you want to process.

● The selected records will be highlighted, and the total number of selected transactions will be visible at the bottom.

Select all Filter for Clover.png

● Use Sync to upload all selected Clover transactions to QuickBooks Online at once.

● Choose Ignore if you do not wish to sync the selected transactions.

● Click Clear Selection to discard the selected records and restart if necessary.

● This option enables you to manage multiple Clover transactions in one go instead of syncing them one at a time.

Step 4: Start the sync review for a Clover transaction

● To sync the transaction, click on Review & Sync.

Select review and sync for Clover.png

● PayTraQer will display the transaction details on the right side of the screen.

● In this section, confirm the Clover transaction date, account, and amount.

Final check for Review and Sync.png

● Also, check the QuickBooks transaction type that is mapped for this record.

● Ensure you are looking at the right Clover payment before proceeding.

Step 5: Confirm the synchronization result

● After the sync, check the Synchronization Details window.

● Make sure the status shows Successful.

● Verify the QuickBooks entries that were created for the transaction, including Invoice and Payment.

Clover Transactions Successfull.png

Step 6: Verify the synced transaction in PayTraQer

● Go to the Synced tab to check the Clover transactions that are already in QuickBooks Online.

● Select Report if you want to see the sync summary.

● If the transaction was mistakenly posted, use Undo to reverse the sync from PayTraQer.

Clover PayTraQer Sync Tab.png

● Use Details to review what was generated for the synced record.

● Click on Open in QuickBooks next to the Invoice or Payment to check the record directly in QuickBooks Online.

Clover Transactions in QuickBooks.png

QuickBooks Transaction FOR cLOVER.png

Step 7: Review past sync

● Go to the Sync History tab to look at previous Clover sync activities.

● Look at the sync date, the types of transactions made, and the count of successful or failed records.

● This page helps you monitor earlier sync operations and verify what was posted.

● If needed, you can use Undo here to reverse a Clover transaction that was synced earlier.

Sync History in PayTraQer.png

Step 8: Open the Clover Sync Settings page

● In the left menu, select Settings.

● Choose Sync Settings from the list of options.

Sync Settings in PayTraQer.png

● Find the Clover connector card on the page.

● Click Change Settings to access the Clover sync configuration.

Change settings for PayTraQer in Clover.png

● Ensure the Clover settings screen is displayed before making any changes.

● This page allows you to manage how Clover sales, items, customers, taxes, and fees sync with QuickBooks Online.

Step 10: Configure the Sales tab

Sales Settings for Clover.png

● Open the Sales tab in the Clover Sync Settings screen.

● Under Accounts, select the bank account for Clover sales deposits in QuickBooks Online.

● Choose the payment method for tracking Clover transactions.

● In the Customers section, decide if PayTraQer should automatically create customers if they don't exist in QuickBooks Online.

● If you prefer not to create separate customers for each transaction, select a Common Customer for Clover sales.

● Use “Customize Customer Matching” if you want PayTraQer to align Clover customers with existing QuickBooks customers based on your chosen matching rule.

● Check any additional options for sales posting, tracking, class, or location if your QuickBooks company utilizes them.

● If your process needs fee-only posting, look at the sync option for skipping sales and only processing related fees.

● After reviewing the sales-related mapping, click “Save”.

Step 11: Configure the Product and Services tab

Product and Service Settings for Clover.png

● Open the Product & Services tab.

● Enable the option to automatically create products or services if the Clover item isn't already in QuickBooks Online.

● Select the type of product or service that PayTraQer should generate, like Non-Inventory, if it suits your workflow.

● Pick the income account that will be associated with the products or services created from Clover transactions.

● In the Match Product section, decide how product matching should occur, such as by Name.

● Utilize Customize Product Matching if you wish to establish precise matching rules between Clover items and QuickBooks products or services.

● If you prefer all Clover sales to utilize a single common item in QuickBooks Online, enable the common product or service option and choose that item.

● Carefully review the product setup to ensure that new and existing Clover items sync properly.

● Click “Save” once the Product and Services settings are finalized.

Step 12: Configure the Tax tab

Tax Settings for Clover.png

● Open the Tax tab.

● Enable automatic tax calculation if you want PayTraQer to automatically compute and apply tax for all Clover sales and expenses.

● Enter the necessary tax percentage for direct payments received if your setup requires tax values in this section.

● Enter the shipping tax percentage if you need to track shipping tax separately.

● Select the common tax code you want PayTraQer to use for Clover transactions in QuickBooks Online.

● Make sure the tax code you select here matches the tax setup in QuickBooks Online.

● Check the full tax mapping before saving, as incorrect tax settings can affect transaction totals and reporting.

● Click “Save” after you finish with the Tax tab.

FAQ

1) Do I need admin access in QuickBooks Online to set this up?

It is advisable to have admin access since you need permission to install PayTraQer, authorize the app, link your company file, and save syncing and mapping settings.

2) Do I need to create customers automatically for Clover sales?

Not always. You can allow PayTraQer to create customers automatically, or you can opt for a Common Customer if you want easier bookkeeping and don't require distinct names.

3) What is the Common Customer in Clover sync settings?

Common Customer allows all Clover sales to be posted under a single chosen QuickBooks customer, rather than generating individual customer records for every sale transaction imported from Clover.

4) How does Customize Customer Matching helps?

This feature allows PayTraQer to align Clover customer information with current QuickBooks customers based on your selected rule, minimizing the creation of duplicate customers during the synchronization process.

5) Can I change the sync mode while Clover is already connected?

No. If Clover or any other connector is active, PayTraQer will display a message prompting you to disconnect all connectors before switching modes.

6) Should I enable automatic product creation for Clover items?

Enable it if Clover items might not already be in QuickBooks. PayTraQer can then automatically create products or services, minimizing the need for manual item setup.

7) Do I need to set tax manually in the Tax tab?

You only need to manually enter tax values if your workflow demands direct payment or shipping tax rates. If not, use the tax options that suit your setup.

8) Can I sync old Clover transactions too?

Yes, go to the Home page and use Download Historical Transactions. Select the date range you need, and let PayTraQer bring in older Clover records for you to review manually.

9) Can I sync multiple Clover transactions at the same time?

Yes. Once you filter and choose the necessary records, use Sync to upload all chosen Clover transactions to QuickBooks Online instead of handling them individually.

10) How do I review a single Clover transaction before syncing it?

Click on Review & Sync for the transaction. This will open a panel on the right in PayTraQer where you can confirm the Clover date, amount, and mapped type.

11) Can I undo a Clover transaction after it has synced?

Yes. If the transaction was entered by mistake, you can use Undo from the Synced tab or from Sync History to undo the Clover sync.

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