How to Connect your QuickBooks with PayPal Online

Quickbooks Errors Solution

PayPal is considered as a tool that allows distinctive payment which is becoming more common as the customers are finding this app to be more suitable in accordance with electronic payments. As a payment processor, PayPal app is considered as a wallet, sales tool, or an online checking account.

Thus, this method also signifies it is confusing and complicated, to manage in QuickBooks. Usually, customers are recommended to handle PayPal as a bank account within QuickBooks.

Benefits of Connecting QuickBooks Online To PayPal App

  • Review of transactions: When Connecting to PayPal, you can evaluate all your transactions before you insert them into QuickBooks.
  • The greater amount of information: Sales receipts will acquire information relevant to the items shipping, discounts, sales, and tax.
  • Track fees individually: When inserting a transaction from PayPal. We will record spontaneously the PayPal fees for you to a price account of your choice so you don’t have to enter by hand.

How does PayPal App work with QuickBooks Online?

Linking PayPal app with QuickBooks Online is an efficient method to make your transactions of PayPal to QuickBooks through the immediate connection with PayPal, we will reclaim the amount which is troubling the transactions to function which you have in PayPal. Now you may edit, label and test the transactions to protect whether it is error-free.

Before Connecting to PayPal

There are a few things you need to do in QuickBooks Online before you connect to PayPal app if you haven’t done so already.

  • In QuickBooks Add your PayPal products and services: To protect the financing and inventory levels the link to PayPal app will recognize the valid products or services for sales according to the item name. In order to function this, you must set up your QuickBooks Items.
  • Establishment of Sales Tax: In order to get linked to PayPal perfectly and track the sales tax accurately, turned on the sales tax in QuickBooks, for the company you require. The Sales Tax Centre or GST center should be turned on if you do not charge even for your customer’s sales tax.
  • In your QuickBooks, if the PayPal services are not mentioned, link it to the PayPal account to choose the default item that is PayPal Sales.

Also Read: How to Fix QuickBooks Won’t Open Error?

Connect QuickBooks Online to PayPal app

  • The First step is to log in QuickBooks Online.
  • From the left menu, click for the Apps.
  • Enter as Connect to PayPal in the Search Apps and press the app.
  • Click the Get App Now button and then choose Let’s do it button.
  • Choose the Give permission to move the data to QB from the PayPal application
  • The email address must be provided that is relevant to the PayPal account and click Next.
    1. You will be requested to build a new one when you do not possess an account
    2. If you build a new account with PayPal, to begin the connection process again, you will be requested to direct back to QuickBooks Online.
  • Type your PayPal necessary qualification and click Sign-in.
  • Choose the Agree and Connect, to approve the connection.
  • When a connection is provided, you can choose Return to Intuit.
  • Choose the account and you will see the PayPal and click Next.
  • Click the Sales tax rate that will be applied to all imported Sales transactions then select Next.
  • If you have the historical transactions, choose the date you wish to start importing and select Done.
  • You are now set up and will find the necessary PayPal connection on the Banking screen

How To Properly Enter PayPal transactions into QuickBooks Online

In this tutorial I’m going to show you how to avoid some common mistakes people make when entering their Paypal transaction into QuickBooks Online.

In this tutorial I’ll be using my Paypal account and a sample QuickBooks company file I use for teaching.

Paypal Transactions in QuickBooks

We’ll start by looking at credit card transactions from a bank account. You can get to this two ways in your own account.

From the main screen you can click on the bank account you’d like from the Bank Accounts box on the right side of the screen.

Opening a bank account in QuickBooks Online

You can also click on Banking in the left-hand navigation menu and select Banking.

Banking Menu in QuickBooks Online

In this example I’m using a $50 payment for training from a company called Score. The payment was made with a Bank of America credit card but was processed through Paypal. You can tell this was processed through Paypal from the Bank Details within the transaction.

Paypal transaction Bank Details

In many people’s QuickBooks accounts I’ll see these Paypal transactions entered with the Vendor/Customer stating who the money went to and the category being what the transaction was for. As you can see here:

Paypal transaction with incorrect vendor/customer and category information

The problem with this method is that it’s not exactly what occurred. Let’s take a look at the Paypal register in Paypal itself for more details.

Paypal Transactions in Paypal

Within Paypal click Summary in the top menu and you’ll see a list of your recent transactions. I have two $50 example transactions at the top of my list.

Recent Paypal transactions

I want to show you a different view of this transaction which I’ll do by clicking on “Activity (including balance & fees).”

Paypal link to Activity (including balance & fees)

In this view you can see that this purchase was from Score Assocation for $50. I didn’t pay a fee and I have a balance of $22.26. The balance is the important part.

Paypal transaction data

That balance of $22.26 is the amount of money I have in my Paypal account. 

Most people don’t think of Paypal as a bank account, but it is. You should think of it like a checking account that has  a balance of $22.26 within it.

From the summary page you can see that balance of $22.26 in the upper left-hand corner.

Paypal summary page showing available balance

But, their are two $50 transactions and the balance remains at $22.26. What’s going on?

To find out I click on the Transaction Type drop down and switch from “Balance affecting” to “All transactions.”

Now those two transactions have a plus sign to the left of the date.

When I click on the plus sign I can see the full transaction.

From this view we can see what actually happened. There was a withdrawal from my credit card of $50 that went to Paypal and then from Paypal to Score. 

It should look the same in QuickBooks but at the moment it looks like it went directly from my credit card to Score without Paypal being involved.

If I view the Paypal register in Quickbooks I can see the balance is $22.26 but I don’t see the transaction from Score.

Paypal register in Quickbooks not showing ALL transactions

When reconciling Paypal in Quickbooks you should log everything that you see under All Transactions in your Paypal account.

This may seem like a lot of extra work and like you’re recording a transaction twice. But, the reason you want to do this is to make sure you’re not missing any expenses or revenue.

Anytime you have a bank account of any type you want to be able to reconcile that account and verify that ALL of your transactions are recorded and nothing is missing.

Properly Handling a Paypal Transaction in QuickBooks

I’m going to go back to the credit card’s register in Quickbooks and delete that $50 Score transaction.

Deleting a transaction in QuickBooks Online.

A warning pop-ups letting me know this transaction was downloaded from my bank’s records, double-checking that I actually want to delete the transaction, but also letting me know  that the transaction will be back on the  Online Banking page. I do want to delete it, so I click Yes. 

I’ll now click on Banking in the left-hand menu and Banking again to get to that Online Banking page. I can see the transaction is back to be reviewed.

I’m now going to change this transaction to a transfer as it’s being transferred from my Bank of America credit card into Paypal.

Recording a transfer in QuickBooks Online

Manually Entering an Expense

I don’t have my Paypal account connected to this QuickBooks file so I will manually enter the expense.

To do this I click the New button in the upper left hand corner then select Expense from the Vendor column.

Manually entering an expense in QuickBooks Online

I now create the expense with a Payee of SCORE, Payment account of Paypal, and I add the $50 transaction in the education category.  Click the “Save and new” button to save the expense.

Manually entering an expense in QuickBooks Online

If I view the Profit and Loss Report you can see there’s only one $50 expense even though the transaction was recorded twice. Once going from the credit card to Paypal, the other going from Paypal to Score.

Profit and Loss report in QuickBooks Online

This is because it was recorded as a transfer and how you should be handling your expenses paid with Paypal.

I hope this tutorial was helpful if you have any questions regarding Paypal transactions and QuickBooks you can send me an email me or book an appointment below.

If you’d like you can watch me walk through this process in the video below:

Connect to PayPal: A New Way to Bring PayPal Transactions Into QuickBooks

How to Integrate PayPal with QuickBooks using PayTraQer?

PayTraQer – QuickBooks and PayPal Integration



Integrating PayPal and QuickBooks is very simple and is just a few clicks away with PayTraQer. SaasAnt PayTraQer – #1 user rated and Intuit trusted automation tool built exclusively for QuickBooks to synchronize PayPal data with QuickBooks Online. PayTraQer synchronizes PayPal Customers, Sales, Expenses, Payouts, Fees, Taxes, etc.. with your QuickBooks Online, keeping your books accurate and precise without the hassles of manual data entry.

Steps for Integrating QuickBooks and PayPal

Connect your QuickBooks company with PayTraQer as mentioned in this article.

Once your QuickBooks account is connected, you will be navigated to the Payment Systems menu screen, where you can select the PayPal tile and click the Connect button. Once clicked, a new window opens up redirecting to the PayPal screen for granting permission. 

quickbooks and paypal integration

The connection to your PayPal account is private and secure. PayTraQer requests just for a READ only connection to your PayPal account and can be disconnected anytime through the settings screen.

paypal and quickbooks integration

Click the “Grant Permission” button, this will authorize the connection and redirect you back to the PayTraQer screen.

You will then have to configure some simple settings for this PayPal account so that your sync is accurate. 

Sales Preferences

PayPal Sales account configuration in PayTraQer:

This setting will govern how your sales transactions will be recorded in your QuickBooks. Default values provided will automatically be created for you in your QuickBooks and is recommended for accurate bookkeeping. 

For more information about each field in the settings, refer to this article.

paypal quickbooks sales preference

Product Settings

PayPal Product configuration in PayTraQer:

This configuration will determine how Products/ Services are synced. If “Create Product/Services automatically” turned ON, then missing items in your QuickBooks will be auto-created during sync. 

For more information about each field in the settings, refer to this article.

quickbooks paypal product settings

Tax Settings

PayPal Tax configuration in PayTraQer:

Enabling this setting will record sync with tax calculation. Otherwise, the tax amount will be added to the transaction amount and recorded without tax.

For more information about each field in the settings, refer to this article.

quickbooks paypal tax settings

Fee Settings

PayPal Fees configuration in PayTraQer:

This setting will govern how the PayPal fee details get recorded in your QuickBooks. You can configure the default vendor, expense category, and expense bank account for creating the expense transaction corresponding to the PayPal fees component.

For more information about each field in the settings, refer to this article.

quickbooks paypal fees settings

Expense Settings

PayPal Exprenses configuration in PayTraQer:

Set the default vendor, expense category, and expense bank account for creating the expense transaction corresponding to the PayPal expense transactions. 

For more information about each field in the settings, refer to this article.

quickbooks paypal expense settings

This is just a quick start setting and the complete set of settings is available under the Sync Settings menu. More on this is available in this article.

quickbooks paypal integration

Recording Historical Transactions from PayPal

Once the above configurations are completed, you are all set up and PayTraQer will automatically pull your last 30 days transactions from your PayPal account.

quickbooks paypal sync

How to connect Paypal to QuickBooks Online

In this guide, you will learn how to connect your QuickBooks Online company to PayPal via Synder. Once you finish your settings, the app will start receiving your PayPal transactions and import data with all necessary details in QuickBooks. Follow easy steps in the helpful guide, and enjoy seamless synchronization.


  1. Start connection from the scratch
  2. Connect PayPal to already existing account
  3. One-click setup (preferred)

Start connection from the scratch

If this is your first integration with Synder you would need to connect your QuickBooks company first. There are 2 ways you can log into the app so 2 ways Quickbooks can be connected to the app.

1. If you log in through QuickBooks Online go to the Apps tab on the left menu bar – – > Find app – – > Synder – – > click on the app and you will be redirected to the app’s page – – > click on the Get app now button – – > Install

Account in the app will be created as well as an organization for this Quickbooks company. Learn more about organizations in this guide [click here].

2. If you create an account in the app directly from the Synder website.

Create Organization where QuickBooks Online and related payment platforms will be located

Select “Connect to QuickBooks” – – > grant the permission

Once QuickBooks is connected you will be on the step 3 to connect Payment Platform

Connect PayPal to already existing account

Now you are on Step 3 where you can Connect payment platform.  If you already have your accounting company connected and you want to access this page follow the steps below:

1. Select Organization needed at the top right
2. Go to Settings on the left menu
3. Click on the Add payment platform button

4. Select PayPal from the dropdown – – > click on the Connect button

After pressing on you will be redirected to the PayPal homepage to grant your permission.

After granting your permission, you will be redirected back to the app. 

One-click setup (preferred)

Now you have an option to go for the quick set-up option. 

1 – I’m ok to start  – Most of the users prefer this set of configurations for syncing their online transactions. You can adjust the most important ones right in this tab and click I’m ok to start and return to settings after if that will be needed.

The app will create a “PayPal Bank Account” in your QuickBooks Online, it is a clearing account to store all your sales and fees in one place. Once PayPal transfers the money to the bank, Synder will also record a transfer from the clearing account to your checking account in your QuickBooks Online for easy reconciliation. Make sure you enabled Payouts and specified there your checking account, then the app will do the bookkeeping for you in full.

2 – Go-step-by-step – You can choose Go-step-by-step and go through detailed configuration. Please check out how to customize PayPal settings in this guide for more detailed synchronization.

“Go step-by-step” button to go through the whole setup
Congratulations! Your account is set and ready to import and sync.

Also Read :: Convert Your Company File to a Newer Version of QuickBooks

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