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Set up and edit VAT settings, codes and rates

This article is for all UK VAT-registered businesses using QuickBooks Online to calculate and submit VAT to HMRC.

From April 2019, all eligible VAT-registered businesses in the UK will have to keep their financial records in a digital form and submit their VAT returns using approved software. Find out whether you're eligible here.

If you are eligible, you'll have to authorise QuickBooks to interact with HMRC. You can choose to do so now, or later, as long as it's completed before submitting your VAT return.

Learn how to:

  1. Set up VAT
  2. Edit settings, codes, schemes and dates
  3. Add an additional tax rate, group rate or custom tax
  4. Show/hide active or inactive codes
  5. How to turn off VAT, MTD and banking feeds
  6. Calculate VAT at line or invoice level

To manage your VAT process, you will need to set it up in the VAT Centre. To access the VAT Centre, start by clicking on VAT on the left navigation.

Setup VAT by entering the following:

  • VAT Registration number
  • Month the current period begins
  • VAT accounting scheme
  • Filing frequency

Once that is done, you are ready to file your VAT. You can always edit your VAT settings after setup.

  1. Go to Taxes, then select Set up VAT.
  2. On the Set up VAT page, select the beginning month of your current VAT period.
  3. Select your filing frequency.
  4. Next, choose your VAT accounting scheme.
    • Standard: also known as accrual, select this option if you count your income when you invoice your customer
    • Cash: select this option if you count your income when you receive money from your customer
  5. Enter your VAT registration number.
  6. If your business is entitled, select the Flat Rate Scheme (FRS) checkbox.​
  7. Select Save.

Your VAT codes are now set up.

  1. Go to Taxes.
  2. Select the Edit VAT ▼ drop-down arrow.
  3. Select Edit settings or Edit rates.
​Make changes to your VAT registration number, changes to your filing frequency, (for example, move from monthly to quarterly), or amend your VAT accounting scheme from a cash basis to the accrual basis.

You can amend some (not all) percentage rates for particular VAT codes. You cannot alter the standard rates for sales and purchases. You can amend the rate of percentage for reduced sales and purchase tax. A drop-down rate history shows the different rates used.

Note: If you want VAT to only show on your transactions and reports, select 'Expenses' in the Account field when editing your VAT settings. If you want VAT to show on the VAT return, choose 'Liability'.

If you change between cash and accrual VAT, we recommend that you switch methods after a filed period has been submitted. Once you select Save, QuickBooks will change the accounting scheme from that day onwards and will retrospectively adjust the liability amounts.

Simply go to VAT settings and then Effective date for the new scheme. The Open Transactions column will appear on the VAT report.

To set up an additional tax rate, group rate, or custom tax to your company, follow these steps.

Note: Once you create a tax agency, you cannot delete it.

  1. Go to Taxes.
  2. Select Add Tax.
  3. Select the type of tax you want to add.
    • Tax rate: add another tax rate for VAT, such as a local tax that is not already included.
    • Group rate: combine multiple taxes and make applying them to your transactions easier. All taxes you include are calculated and charged at once, but we track them separately for you.
    • Custom tax: add a tax agency and a tax percentage, such as an environmental levy, hotel, or petrol tax.
  4. Select Save.

To view your new VAT agency, click on the drop down arrow next to the current VAT agency or click the arrow on the right side of the Taxes dashboard.


If you can't see a particular code in QuickBooks, they may be inactive. To active codes in QuickBooks simply got to:

  1. Go to the Taxes page in QuickBooks, select Edit VAT and then Edit Rates.
  2. Select the gear icon above VAT rates and select Include inactive. This will show a list of all the currently inactive codes.
  3. Use the toggle feature against the VAT code you want to activate/deactivate.

If you’ve deregistered from VAT you will want to turn off VAT in your settings too. This will stop VAT from showing in future transactions and bank feeds, and will save you time from having to update these manually in QuickBooks.

While you won’t be able to turn off VAT completely, there is a quick and simple way to default your transactions to show ‘No VAT’ and here’s how:

  1. Click the Gear icon and select select Account and settings.
  2. In the Advanced, select the pencil Edit icon in Accounting.
  3. Change the Default tax selection to No VAT.
  4. Select Save and then Done.

Now when you go to create a transaction in QuickBooks, the VAT column will be hidden under the Default tax rate selection options.

If you have bank accounts connected to QuickBooks, you will need to create a new rule to ensure transactions are set to No VAT in your banking feed.
  1. In Banking, and select the Rules tab.
  2. Select New rule.
  3. Name the new rule with something memorable such as ‘VAT deregistration money in’.
  4. Select Money in.
  5. Change Description to Amount.
  6. In the next field, select Is greater than.
  7. Enter 0.01 in the value field.
  8. Select No VAT for the tax rate.
  9. Repeat the steps for Money out.
  1. Go to the gear icon.
  2. Select Account and Settings.
  3. In Advanced, go to Making Tax Digital.
  4. Select Learn how to Disconnect and follow the steps.

According to HMRC's VAT guide, if you calculate VAT at line level or invoice level, you must not round the VAT figure down. But, you can round up (or down) each VAT calculation.

  • Round down if the VAT on any transaction comes to less than 0.5 of one penny
  • Round up if the VAT comes to 0.5 of one penny or more

Read the HMRC trader's records manual for more information.

More helpful links

Common VAT codes 

Submit a VAT return 

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