Customize your Synder PayPal Settings (QuickBooks Online)

Overview

With your company and accounts connected, you can start customizing the PayPal–QuickBooks Online integration settings. These settings determine how QuickBooks Online records transactions, invoices, fees, expenses, and payouts.

PayPal settings are organized into the following sections:

Plan availability:

• * Available from the Essential plan and higher
• ** Premium feature available only on Pro and Premium plans

How to Access PayPal Settings

To access your PayPal settings in Synder:

Option 1: From the main menu

1. Select the appropriate organization from the top-left corner
2. Click Settings in the left-hand menu
3. Choose PayPal from the dropdown list

Option 2: From Organization Settings

1. Click the person icon in the upper-right corner
2. Select Organization settings
3. Click Sync settings under PayPal

1. General settings

1. Auto-Import – When ON, Synder automatically imports transactions from your PayPal integration without affecting your sync balance or syncing them to Xero. When disabled transaction imports are manual on Synder.
2. Auto-sync – When ON, Synder automatically syncs transactions after import. When OFF, you will sync transactions manually by individually selecting them from the platform transactions tab
3. Skip synchronization for duplicated transactions * – When enabled, Synder skips transactions that already exist in Xero with the same ID, preventing duplicates.
4. Process transactions in multiple currencies – When enabled, Synder syncs all transactions regardless of currency. When disabled, Synder syncs only transactions in your home currency.
5. Automatically Archive Pending Transactions – When enabled, Synder removes pending PayPal transactions that PayPal never finalized, keeping your Synder dashboard clean.
6. Shipping item name* – Enter the PayPal item name used for shipping. Use this setting only if shipping appears as an item in your sales transactions. If shipping is recorded in the PayPal shipping field, no additional setup is required. 
7. Apply location ** – When ON, select a QuickBooks Online location to assign to synced transactions.
8. Timezone – Displays your PayPal account’s timezone to help match dates between PayPal and QuickBooks Online.

2. Sales

1. Clearing account – A buffer account where Xero sales receipts, refund receipts, fees, and payments are deposited before being transferred to your main accounts.
2. Enable QuickBooks Doc Numbers – When ON, transactions follow the standard QuickBooks document numbering sequence. When OFF, Synder assigns the DocNumber using the number from your payment processor.
3. Apply generic customer * – When ON, all transactions are assigned a generic customer name to keep your QuickBooks Online customer list organized. Choose or enter a default name, such as “PayPal Customer,” to apply to all transactions.
4. Payment Method – Select the default payment method (cash, check, credit card, or PayPal) that will be used for sales receipts, refund receipts, payments, and expenses.
5. Sync discounts as products ** – Discounts can be synced as separate products, such as “PayPal Discount,” for detailed tracking.
6. Sync only Payments/Deposits * – Enable this setting to record order-related payments as Receive Payments instead of Sales Receipts or Invoices and Payments. You can then apply them to invoices manually. See our guide for more details: Syncing PayPal Shopping Cart Payments as Deposits/Overpayments in Synder.
7. Discount product account – Select the account to use when creating a new discount product in your books. 
8. Payment method mapping * – Synder retrieves the payment method used in PayPal and includes it in the transaction description. You can use this information to map the payment method in QuickBooks Online.

3. Invoices

1. Apply payments to unpaid Invoice/Bill transactions * – When ON, payments that match an unpaid invoice are applied automatically, ensuring invoices are closed correctly.
2. Cancel sync if there is no matching open invoice found for a payment * – If a payment doesn’t match any open invoice, it won’t sync, preventing incorrect entries.

4. Products and Services

1. Record transactions with Original/Common product/service name and SKU – Choose whether Synder records transactions using the original product name or a common product name. Synder matches original names to existing products in your accounting software by name or SKU and creates a new product when no matching product exists. Common product names help standardize future transactions.
2. If original product is missing – If the original product is missing in the sales platform, Synder will use the item or SKU.
3. Configure product search priority – Allows you to define whether Synder searches by SKU or product name first when matching products between PayPal and QuickBooks Online. See our guide for more details visit Product Search Priority.
4. If the matching product is not found * – If the matching product doesn’t exist in QuickBooks Online, Synder can either create a new product or cancel the transaction sync.
5. Assign product type – Select the product type for newly created items: Non-inventory, Inventory, or Service. See more details about the inventory below.
6. Assign income account – Select the income account that will be used for this product.
7. Assign expense account – Select the expense account that will be used for this product.

Inventory

Synder supports inventory tracking, but inventory items must already exist in QuickBooks Online, and their names must exactly match the names in your payment processor. Synder cannot create inventory items because QuickBooks requires a Quantity on Hand (starting stock level), which Synder cannot access. Existing inventory items will sync correctly, and QuickBooks will automatically update their stock levels. See our guide for more details Managing Products and Services with Synder – Per Transaction Sync.

1. Select an income account to track sales for the inventory product.
2. Select a Cost of Goods Sold account to track the cost of the inventory product.
3. Select the inventory start date that Synder will use when creating the new inventory product. Please note that posting sales of inventory products, which occurred before the set inventory start date, will fail.
4. Select the initial Quantity on Hand that Synder will use when creating the new inventory product.
5. Select an inventory Asset account to track the cost of purchased products.
6. Select an inventory adjustment account to track shrinkage or different write-offs.

5. Product mapping *

Synder can identify existing products in your accounting company and apply them to transactions. If product names in your payment system and accounting company don’t match 100%, fill in the product names from your payment platform in the right field to map it to product names from your QuickBooks Online in the left field. Check out an additional guide about Product mapping feature.

6. Taxes tab settings

Sales taxes settings for US-based QuickBooks Online companies

Most QuickBooks Online users in the U.S. use Automated Sales Tax, which allows QuickBooks Online to apply sales tax automatically based on the sale or company address. QuickBooks Online calculates the tax rate automatically.

1. Apply Taxes – Enable this setting to have Synder record taxes in the tax field for accurate reporting. Leave it disabled if you prefer taxes to be recorded as a line item.
2. Marketplace Facilitator Tax Category – Synder records marketplace-remitted taxes in both the sales and expense sections of your transactions for accurate reporting of your lack of tax liabilities. Use this setting to choose the account for tracking marketplace facilitator tax. See our guide for more details Marketplace Facilitator Tax.
3. Track marketplace facilitator tax as your own payable – When ON, Synder records marketplace-remitted taxes as your tax payable in the sale and deducts them as an expense. When OFF, Synder records these taxes as a line item in the sale and deducts them as an expense without affecting your tax payable liability. See our guide for more details Marketplace Facilitator Tax.

Sales taxes settings for Non-US-based QuickBooks companies

When your payment processor calculates taxes, Synder automatically records them in QuickBooks Online. If your payment processor (such as Stripe, Square, or PayPal) does not calculate taxes, use Synder tax settings to apply and record taxes in QuickBooks Online. See our guide for more details on how sales tax works in Synder.

7. Fees

1. Clearing account – Select the clearing account where PayPal fees are recorded. Use the same account as the Sales clearing account to keep all related transactions consistent.
2. Vendor – Select a QuickBooks Online vendor to assign PayPal fees. Choose an existing vendor or enter a custom name to group all PayPal fees under one vendor.
3. Category – Select the expense category in QuickBooks Online for PayPal fees to track and report processing costs accurately.

8. Expenses

1. Clearing account – Select the clearing account where expenses are recorded. Use the same account as the Sales clearing account to keep your records consistent.

2. Generic Vendor – Synder assigns all expenses to a default vendor instead of creating a new vendor for each transaction. Choose an existing vendor or enter a custom name.

3. Category – Select the expense category in QuickBooks for these transactions to track and report expenses accurately.

9. Payouts

The Payouts tab tracks PayPal payouts—bulk transfers from your payment processor to your bank (daily, weekly, monthly, etc.). Synder records these as transfers from the clearing account to your checking account. Syncing payouts with sales and expenses helps reflect actual cash flow and simplifies reconciliation.

1. Process payouts – When ON, Synder tracks PayPal payouts and creates transfers to your checking account. When OFF, payouts are not synced, and the clearing account won’t be cleared automatically.
2. Transfer Funds To – Select the Xero checking account where the PayPal payouts are deposited by Synder.

10. Multicurrency

Synder supports multicurrency. While Synder doesn’t perform currency conversions itself, it transfers conversion rates from your payment processor to QuickBooks Online to avoid discrepancies. Conversion rates can differ between QuickBooks Online and PayPal on the same day, so recording the rate from the original source is important.

Synder automatically enables multi-currency when you enable it in QuickBooks Online. Set up your accounts to reflect real-world money flow—for example, use separate checking accounts if payouts are in different currencies. Typically, payouts are in a single currency, while sales can occur in multiple currencies.

You can find how to customize Multiple Currencies here in the Multicurrency tab. Check how to Synchronize Multicurrency Transactions in QuickBooks Correctly.

Additional Settings

Use the “Create additional settings” option only if you want to categorize different types of transactions. Use this feature if you’re tracking some transaction types differently.

Reach out to Synder Team via online support chat or email with any questions you have – we are always happy to help you!