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Quickbooks Online Integration
Setting Up Your Quickbooks File
Setting Up Your Quickbooks File

Configuring the integration between Quickbooks Online and Crystal.

Jeff Hanrahan avatar
Written by Jeff Hanrahan
Updated over a week ago

Setting up your QuickBooks file

Before connecting with Crystal there are a few things you can do to prepare your QuickBooks file for how Crystal syncs your sales and inventory data. You can always change these later as well while testing or actively using the integration.

Chart of Accounts

Crystal will default to using many of the common accounts used in QuickBooks such as Accounts Receivable and Accounts Payable, even if your QuickBooks file is brand new. You’ll be able to select and change these accounts if you like, which we’ll cover in more detail in the configuring accounts and products section.

There is one account that Crystal cannot create or use automatically which will need to be set up in QuickBooks: your “Deposit To” account. This is typically a Bank type account that represents the operating account the business uses to deposit cash and credit card funds.

The “Deposit To” account may also be an Other Current Asset account, such as Undeposited Funds, but that’s not typically recommended. Undeposited Funds expects each transaction to be matched to a bank feed transaction before being deposited during reconciliation. This is an arduous manual process that is overly time consuming for most accountants or bookkeepers. Using the direct deposit Bank account allows flexibility to match daily or weekly deposits with entries made by Crystal.

Company Preferences (Account and Settings)

Crystal uses many of your preferred settings that are already configured in your QuickBooks file under the Account and Settings area (accessed within QuickBooks Online by going to the Gear Icon (Icon) in the top right > Your Company > Account and Settings). We’ll walk through each of the settings that can be used so you can validate any changes that may need to be made.

Sales section

Preferred Invoice Terms - When a customer pays over time for a transaction through Crystal, the transaction may have terms applied to the “On-Account” payment within Crystal. If this is set on the transaction in Crystal, the same terms will be applied to the invoice that is created in QuickBooks. On the other hand, if a transaction that is paid over time does not have terms set in Crystal, the invoice generated in QuickBooks will use your preferred terms set here.

Custom Transaction Numbers - Crystal can create a variety of transactions including Sales Receipts, Invoices, Payments, Refund Receipts, Credit Memos and more. If this preference is enabled, Crystal will use the same transaction number that is used on the sale in Crystal as the document number in QuickBooks.

Setting Custom Transaction Numbers in QuickBooks:

Alternatively, if this preference is disabled, Crystal will use the numbering that is automatically used by QuickBooks. In this case, we’ll also include the related Transaction ID from Crystal as part of the memo or message field within the transaction in QuickBooks as an alternate lookup so that transactions can still be matched together easily.

Custom Transaction # Enabled:

Custom Transaction # Disabled:


Purchase orders - If use purchase orders is enabled, any purchase orders created in Crystal will also be synced to QuickBooks. Purchase orders are optional in QuickBooks and in Crystal. Merchandise Received receipts in Crystal will be synced separately from purchase orders to track inventory expenses and asset value, but if a purchase order is used, the received receipt will be attached as the purchase order is received.


Close the books - Crystal does not use this preference, but it should be noted that if this is enabled and a month is closed in QuickBooks, Crystal will not be able to sync transactions from that time period.

Categories: Track classes - Optionally, Crystal can use classes to track product sales and expenses by category. If this setting is enabled and set to “Assign classes: One to each row in transaction” product categories in Crystal will be included as the class for line items of products on sales and refund transactions. This can be used to run reports such as P&L by Class. We’ll discuss products more in the configuration section.

Categories: Track locations - Similar to classes, Crystal can optionally use QuickBooks “Locations” to create transactions per each store location that has been configured in Crystal. If this setting is enabled and set to use the location label Location, Property, Store, or Territory, Crystal will set the location on each transaction it creates to the corresponding store location from the point of sale where the transaction was generated.

When Classes and Locations are enabled in QuickBooks, Crystal will add the relevant information from the transaction details like this:

Automation: Automatically apply credits - When a customer requests a refund for store credit, Crystal will generate a credit memo on the customer’s account to be used on a future purchase. When a future purchase is made by the customer and store credit is requested as the payment method, Crystal will apply the previously generated unused credit to the invoice of the new sale. As such, it is recommended that this setting be disabled. If Crystal creates a credit memo, and a transaction is edited in QuickBooks manually, the credit may be automatically applied incorrectly by QuickBooks and will not be available for use on future transactions.


If the business has been using QuickBooks Online, taxes are most likely already configured for your reporting agencies and tax rates. However, if this is a fresh QuickBooks file, or you are testing the integration on a sandbox account, you’ll need to configure the basics of how taxes are reported in QuickBooks.

In the left navigation menu of QuickBooks, click on Taxes > Sales Tax and select Use Automatic Sales Tax. QuickBooks will walk you through configuring your company file for your home jurisdiction and reporting agency, and will let you set up additional jurisdictions. In order for Crystal to sync any sales tax, this needs to be configured with at least one reporting agency in QuickBooks.

We’ll discuss taxes in more detail in the configuring tax liability section, but at a basic level, Crystal will use mappings that you specify for each point of sale store location to override QuickBooks automatic tax calculation and deposit the tax collected to the assigned agency for remittance.

Each of the aforementioned sections can be updated and refreshed within Crystal at any time if you make any changes to your business. Now that we’ve initially reviewed them, you are ready to connect to Crystal.

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