Julie,
For some guidance have a look at the following from HMRC: http://www.hmrc.gov.uk/manuals/bimmanual/bim51520.htm
Does the company's sales invoice cover the full contract value and they get paid it less the retention or is the sales invoice for the contract value less retention? Either method seems to be acceptable to HMRC so the next step is how to deal with the bookkeeping.
In the former case, full value invoice, the payment would be offset against the relevant invoice leaving a residual value (the retention). This due amount will sit on the account and act as a reminder. As your company is on VAT cash accounting it will not distort the VAT payments to HMRC. After the retention period is over, you would chase the retention. If it is paid, VAT will be due and dealt with as normal under VAT cash accounting. The down side is that the retention will form part of the profit and is therefore taxed in the year of the invoice whereas it is only realised in the year of payment. If the retenion does not get paid, it should be written off in due course.
In the latter case, invoiced at full value less retention, payment will fully offset the invoice. There is no residual value acting as a reminder of retention due. It is imperative to then keep a list of retentions due, with dates when due, and invoice these on due date. Practically I would always chase the payment to be fairly certain that payment will be forthcoming before invoicing the retention.
I assume that CIS is not also involved so have not mentioned it in my response.
Paul
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