How to connect Stripe to QuickBooks in easy steps

Running an ecommerce business means juggling a thousand moving pieces. Between nurturing client relationships and fulfilling high-order transaction volumes, recording and reconciling financial admin work is a big challenge.  

Have you ever thought about automating the flow of payment data directly into your accounting records? Yes! - Excellent choice! No! - Don't worry, we've got you covered. 

The solution begins with connecting a financial infrastructure platform like Stripe with accounting software like QuickBooks. 

One Reddit user wrote- “Switching to Stripe could solve the issue by automatically handling sales receipts, customer/product details, and recurring payments”. His statement backs that Stripe is the best choice for integration with QuickBooks as compared to other financial platforms like Square.

By learning how to connect Stripe to QuickBooks, you'll create a financial ecosystem that runs on autopilot.

In this article, we’ll walk you through a simple, step-by-step process to establish this connection, ensuring a smooth financial setup.

Understanding the benefits of Stripe QuickBooks integration

The total transaction value in the digital payments market is projected to reach US$20.09tn in 2025. With such a tremendous increase in digital payment transactions, you might face financial management challenges. 

If you are tired of managing your business finances in a complex digital environment, integrating Stripe with QuickBooks is the upgrade you need. 

Let’s understand how establishing the connection of this duo can make your financial operations seamless:  

1. Automate payment recording

Every time a customer pays through Stripe, the transaction is automatically synced to QuickBooks. Integrating these two platforms ensures you don't need to do any manual data entry or double work—your sales, fees, and refunds are always up to date

2. Seamless invoicing and faster payments

Create invoices in QuickBooks with “Pay Now” links powered by Stripe. Customers can pay instantly online, and once payment is received, the invoice is automatically marked as paid in your books. This means less chasing and faster cash flow

3. Real-time financial insights

With all your payment and accounting data unified, you get a real-time snapshot of your cash flow, sales, and outstanding invoices. This makes it easy to spot trends, manage expenses, and make smart decisions on the fly

4. Effortless reconciliation

Stripe deposits and transactions are matched with QuickBooks entries, making month-end reconciliation a breeze. You spend less time searching for missing payments and more time focusing on other core business activities 

5. Reduce errors and save time

Automation slashes the risk of human error and saves you numerous hours each week. You can reinvest that time in growth or customer service instead of bookkeeping

6. Enhanced accuracy for tax and compliance

With every transaction precisely logged, your records are audit-ready, and tax preparation is simplified. It means no more scrambling for receipts or worrying about misreported revenue

7. Scalable for growing businesses

As your transaction volume grows, the integration keeps up with everything from a handful of payments to thousands each month without missing a beat

8. Unified customer data

Sync customer information between Stripe and QuickBooks to keep your records consistent and avoid duplicate entries. This ensures your financial and customer data always align

How to connect Stripe to QuickBooks

Connecting Stripe to QuickBooks is a straightforward process, but it requires a third-party integration app since there is no direct, native connection between the two platforms. 

Here’s a step-by-step process that will guide you to set up the integration and automate your payment and accounting workflows:

Step 1: Prepare for integration

The first step in integrating these two platforms is to ensure you have active accounts on Stripe and QuickBooks. If you haven't already, sign up for Stripe and QuickBooks.

Next, you'll need your Stripe account credentials, including your API keys (available in the Stripe dashboard), and your QuickBooks Online login details.

Step 2: Execute the integration process (App integration)

Now, it's time to bring Stripe and QuickBooks together in perfect harmony. Here's the step-by-step process:

1. Log in to your QuickBooks Online account and select the "Apps" section on the left-side navigation menu.
2. Search for the Stripe integration app.
3. You’ll be asked to log in to both your QuickBooks and Stripe accounts to authorize the connection. This typically involves granting the app permission to access and sync your data securely.
4. Follow the prompts to connect your Stripe account to QuickBooks Online. You'll need to provide your Stripe API keys during this process.

Note: Compare different third-party integration tools by looking at their features and reviews, and choose the right one for your business. Webgility is one platform that is trusted by innumerable users and offers helpful features to streamline your finances. 

Step 3: Configure integration settings

Once the initial connection is established, you'll have the opportunity to customize the integration to suit your business needs. Here are some key settings to consider:

• Automatic invoice creation: Enable this feature to let QuickBooks automatically create invoices for successful Stripe charges, streamlining your billing process
• Payment sync: Ensure that payments received through Stripe are accurately reflected in your QuickBooks accounts, maintaining a real-time financial overview
• Product and service mapping: Map your Stripe products and services to their corresponding QuickBooks items, ensuring consistent tracking and reporting

By taking the time to configure these settings correctly, you'll save countless hours and minimize the risk of errors.

Step 4: Enable auto-sync 

Some ecommerce automation tools support automatic syncing of new Stripe transactions into QuickBooks. Turn on this feature to keep your books up to date without manual intervention. You can also import historical data from the past months or even years. 

With this integration, you can sit back and marvel at the seamless flow of data between the two platforms. Stripe charges will automatically sync with QuickBooks, updating your financial records in real-time. 

How to record and reconcile Stripe payments in QuickBooks

Recording Stripe payments in QuickBooks is essential for accurate financial reporting. However, doing this can be challenging since Stripe processes payments, deducts fees, and transfers net amounts to your bank account. 

Here's a comprehensive strategy for recording Stripe deposits and regularly reconciling your bank account to ensure your books are ready for tax filings or audits:

Step 1: Create a Stripe Clearing Account

First, set up a dedicated bank account in QuickBooks Online to track your Stripe funds:

1. Go to Accounting > Chart of Accounts
2. Click "New" to create a new account
3. Select "Bank" as the account type
4. Name it "Stripe" or "Stripe Clearing Account"

This account will act as a holding account that reflects the funds Stripe maintains before transferring to your actual bank account.

Step 2: Export Stripe transaction data

When you need to record transactions:

1. Log into your Stripe account
2. Go to "Reports" or "Balance"
3. Change the date range to your preferred period (weekly, semi-monthly, or monthly)
4. Download the CSV report of transactions
5. Save this file in a dedicated folder for your records

Step 3: Record gross sales and fees in QuickBooks Online

Always ensure you enter the gross sales in QuickBooks before deducting any Stripe fees. For this, you must: 

1. Create an Invoice:
2. In QuickBooks Online, click the "+ New" button and select “Invoices”
3. Enter the gross sale amount and customer details.
4. Mark the invoice as paid if you've already received the payment via Stripe.
5. Sales Receipt (if you don't issue invoices):
6. Select "Sales Receipt" to record the income
7. Use the proper income account and enter the GROSS amount (before fees)
8. Add any relevant class or location tracking
9. Save the sales receipt

Step 4: Record Stripe fees as an expense

1. Click "+ New" again and select "Expense"
2. Enter "Stripe" as the payee
3. Select your Stripe Clearing Account
4. Under "Category," select Bank Fees or create a new account called "Stripe Fees."
5. Enter the fee amount deducted by Stripe.
6. Save the expense

Step 5: Record transfers to your bank account

When Stripe transfers funds to your bank account:

1. Click "+ New" and select "Transfer"
2. Select "Transfer Funds From" your Stripe clearing account
3. Select "Transfer Funds To" your actual bank account
4. Enter the transfer amount (this should match the amount appearing in your bank statement)
5. Use the Stripe payout ID as the reference number
6. Save the transfer

Step 6: Reconcile your Stripe account

Now that you have recorded the sales, fees, and deposits, your Stripe Clearing Account should balance to zero. To verify this: 

1. Go to “Chart of Accounts” and find your Stripe Clearing Account. 
2. Ensure that the balance is zero, indicating that all sales, fees, and deposits have been properly recorded and matched.

Step 7: Reconcile your bank account

1. Use the Stripe Balance Summary report you downloaded
2. In QuickBooks, go to Accounting > Reconcile
3. Select your Stripe clearing account
4. Enter the ending balance from your Stripe report
5. Match the transactions in your Stripe account with your QBO records

Here are some important considerations you must not overlook when reconciling your Stripe payments in QuickBooks:

• Always record the gross sales amount to avoid understating your revenue
• Record fees separately as expenses for accurate profit reporting
• Create a consistent schedule for recording Stripe transactions (weekly or monthly)
• Keep all Stripe reports organized for reference and audit purposes
• Always reconcile your Stripe clearing account to ensure accuracy

Summing up

The first step—how to connect Stripe to QuickBooks. 

The second step—how to reconcile Stripe payments in QuickBooks. 

Now, an important thing here is to know both these steps. This guide will help you easily integrate this powerful duo and manage Stripe payments in QuickBooks that requires attention to detail and a systematic approach.

However, for businesses looking to scale, the manual method becomes unsustainable.

Wondering how you can make this tedious manual process short and easy? This is where third-party integration tools like Webgility can save considerable time by:

• Automatically creating sales receipts for each Stripe payment
• Recording processing fees as expenses
• Creating transfers between your Stripe clearing account and bank account
• Simplifying the reconciliation process with accuracy

Stop manual entry—Let Webgility take charge of your finances! 

This no-code automation tool is an excellent choice for connecting Stripe and QuickBooks, which is one of the reasons why numerous businesses trust Webgility. 

It automatically syncs transactions, including sales, fees, and refunds, between Stripe and QuickBooks, so you’ll know exactly what you’ve paid in marketplace fees, payment processor charges, and shipping costs. Using this tool, you’ll also know what you’ve charged in sales tax and validate that amount for easier filing. 

Ready to transform how you manage your accounting workflow? Get started for free today!