If you’re using PayPal in your business, you know how useful it can be to accept payments quickly. But when it comes to bookkeeping, PayPal can also be a bit… messy.
Maybe you’ve tried reconciling your PayPal activity in QuickBooks and wondered, “Where did this fee come from?” or “Why don’t these numbers match?”
In this post, you’ll learn exactly how to get your PayPal bookkeeping data, including statements and transaction history with a running balance.
We’ll also talk about which formats are most helpful for reconciliation and what to do if you’re missing something or double-counting a transaction.
Whether you’re a bookkeeper, small business owner, or just trying to clean up your records, this guide will walk you through everything you need to know.
Why Accurate PayPal Bookkeeping Data Matters
When you use PayPal for business transactions, you’re dealing with more than just deposits. You’re handling:
Incoming payments
Fees
Refunds and chargebacks
Currency conversions
Transfers to your bank
All of this needs to be recorded correctly in your bookkeeping system, whether it’s QuickBooks Online or another accounting tool.
If you only record net deposits, you’re missing critical pieces of your financial puzzle—like gross income and fees.
To do it right, you need complete and clean PayPal bookkeeping data—ideally with a running balance to reconcile your books accurately.
Log in to Your PayPal Account
It might sound obvious, but make sure you’re logging into the correct PayPal account—especially if you manage multiple businesses or accounts.
Go to PayPal.com and log in.
Click Activity in the menu across the top.
Download a Transaction History Report (with Running Balance)
For reconciliation, the most useful report is the one that includes a running balance. That way, you can go line by line and compare your PayPal balance to your QuickBooks balance.
Here’s how to download it:
From the Activity tab, click All Transactions.
- Click the download button on the right.
- Choose Balance affecting from the Transaction type drop-down.
Select the time period you want to download from the Date range drop-down.
Select CSV from the Format drop-down.
- Click Create Report.
Once downloaded, open your CSV and take a look at these key columns:
Date
Type (Checkout, Payment, Withdrawal, Deposit, etc.)
Gross amount
Fee
Net amount
Balance
The Balance column is the running balance we were looking for. It does not appear on the PDF version of this report.
Use this report to spot discrepancies and make sure you’re entering both income and fees properly in your accounting software.
Download a PDF Statement (If You Need One)
If you also want a traditional monthly statement-style PDF, you can get that too.
How to download a statement PDF:
From Activity, click All Reports.
Select the Payments tab.
Click Statements – monthly and custom.
Find the month you need in the History section, or select a date range and click Create report.
- Click Download in the PDF column for the date range you’re looking for.
This document includes:
Beginning and ending balances
Summary of inflows and outflows
Totals for payments and fees
It’s useful for general review, but less helpful if you’re trying to reconcile line-by-line.
Step 4: Use PayPal Data for QuickBooks (The Right Way)
Once you’ve got your PayPal bookkeeping data, how you use it depends on your workflow.
If you’re entering transactions manually in QuickBooks, use the gross amount and the fee as separate line items:
Example:
$399 Income
$20 PayPal Fee
$379 Net Deposit (this is what gets deposited into your bank account)
Don’t just enter the $379! That will understate your income and ignore the fee expense.
💡 Pro Tip: If you’ve connected PayPal to QuickBooks using a bank feed or app, you may be able to skip manual entry. Just make sure the connection is accurate, and don’t double-enter by manually adding items unless you have to.
Bonus Tip: Double-Check with the Running Balance
When things go off the rails—maybe you forgot to record a refund or added the same transaction twice—the running balance is your best friend.
Compare your QuickBooks balance to your PayPal CSV’s running balance every few transactions:
Does it match on the 1st?
Still good on the 5th?
Suddenly off on the 8th?
Now you know where to start looking for the error.
Common PayPal Bookkeeping Mistakes to Avoid
When it comes to PayPal, it’s easy to make a mess. Here are a few things to watch out for:
Only recording the net deposit instead of gross income + fees.
Missing refunds or chargebacks.
Overlapping imports and manual entries, leading to duplicates.
Not reconciling—trusting PayPal’s total without verifying.
Use your downloaded PayPal bookkeeping data to avoid these problems and keep your books clean.
What If You Still Feel Lost?
I get it. Sometimes it’s not about downloading the data—it’s about knowing what to do with it.
If you’re struggling with messy PayPal records or need help setting up your import workflow, I’ve got options for you:
📅 Book a one-on-one session to walk through your PayPal data together.
🎓 Get my PayPal Bookkeeping in QuickBooks Online course.
📧 Reach out for a done-for-you quote if you’d rather have someone clean it up for you.
Final Thoughts: Stay Ahead with Good PayPal Bookkeeping
PayPal is a fantastic tool for small businesses and freelancers, but it can be tricky to track without the right setup. By downloading the correct PayPal bookkeeping data, reviewing your running balance, and recording both income and fees, you’ll keep your books accurate and ready for tax time.
Whether you’re importing manually, using a bank feed, or somewhere in between, understanding how to access and use PayPal reports is a key part of your financial workflow.
☕ If you found this helpful, you can say “thanks” by buying me a coffee: https://www.buymeacoffee.com/gentlefrog
Watch video walkthroughs below:
