I have a client that is using the VAT Margin scheme. Can anyone assist in how to record this in Quickbooks.

Currently, QuickBooks Online UK doesn't have a built-in VAT Margin Scheme tool, so you'll need to track your profits and calculate the VAT by hand. To record this, first keep a separate digital stock book (like a spreadsheet) to log each item's buy price, sell price, and profit as HMRC requires.

When you buy an item, log it as an Expense or Bill. Your choice of tax code depends on your scheme. Use a 0% tax code if you're on the Global Accounting Scheme to put purchase values into Box 7, or choose No VAT/Outside Scope code if you're on the Standard Scheme to update those totals yourself.

Lastly, create your customer Invoice or Sales Receipt without listing VAT as a separate line, figure out the 1/6th VAT on your profit margin by hand, and use the VAT Adjustment in QuickBooks to manually add that tax to Box 1 before you file your return.
 

For full record rules details on the VAT margin scheme, check out the official HMRC website: Using the global accounting VAT margin scheme.

Drop a reply if anything comes up or if you have other concerns.