Hi
I run my own ltd company from home and charge it some rent because of the space it uses.
Last year when it came to preparing my own personal self assessment I included the rent received the UK Property Section of my self assessment. The figure was entered in box
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Taxable income
You are effectively charging the company the same amount of rent that it is costing you to provide that space for the company use. This is why the figure you enter for expenses is the same as the income figure.
On your self assessment return you should really be breaking down the running costs of your home to include them in the relevant boxes of the return, rather than just "other expenses", but the effect is the same: you are providing your home to your company but not making a profit on it, so there is no taxable income from the property.
With no net taxable income there should be no effect on tax credits.
Be careful to ensure that no part of your home is used exclusively for business use, or there can be CGT consequences if you later sell.