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You can only claim First Year Allowance or Annual Investment Allowance for 100% of the cost of the car in the year you bought it I'm afraid. You could claim a reduced FYA or AIA for the first year and writing down allowances in future years. I'm not sure your mortgage people would understand that the one off big capital allowance claim in year 1 which would significantly reduce your taxable profit was just that, a one off.
Instead, you might claim writing down allowances whereby you claim 18% of the cost of the car in year 1 and 18% of the reduced balance in years 2, 3, 4 et seq until you have written off 100% of the cost of the car. So, in year one on a £20,000 car, you could claim a writing down allowance of £3,600 which would leave you with a written down value of £16,400. In year 2, you could claim a writing down allowance of £2,952 which would leave you with a written down value of £13,448.
Take a look here for information on First Year Allowances and the Annual Investment Allowance.
I hope this helps but let me know if you have any further questions.
You never need to claim the entire capital allowance available. You can claim a reduced sum which leaves more to claim in later years.
You can claim a bit of AIA in year one and WDA at 18% of the balance. AIA is only available on low emission cars, however. I don't think you can claim both a first year allowance and a writing down allowance as you can with AIA.
I'd claim FYA not AIA for your car unless it is a black cab. AIA s normally restricted to cars that are black cabs or that have been converted for driving instruction. As far as I can see you cannot mix FYA and WDA.
The danger with a big initial claim is that there may be clawback of allowancer if you sell for a high resale value.