If a bill has been coded to a fixed asset account and has a value over £2000 including VAT, the system will include this on your next VAT return in box 4 and 7.
As per HMRC guidance:
If you use the Flat Rate Scheme, you can reclaim the VAT you have been charged on a single purchase of capital expenditure goods where the amount of the purchase, including VAT, is £2,000 or more.
You deal with these capital expenditure goods outside the Flat Rate Scheme. This means that you claim the input tax in box 4 of your VAT return.
If the supply is:
- more than one purchase
- under £2,000 including VAT, or
- of services
then no VAT is claimable, as this input tax is already taken into account in the calculation of your flat rate percentage.