In 2015, Skinner was charged with: two counts of making a false instrument; one count of fraud; and one count of false accounting between 2004 and 2009. In his subsequent trial at Southwark Crown Court, the jury heard that he had claimed almost £500,000 for support staff over a five-year period.

In evidence, it was alleged that Skinner had made payments of £10,000 a month to his wife from December 2007 until July 2009, which entitled him to claim secretarial or parliamentary assistance allowance. It is also alleged that he created a fake letter, for a payment of £5000 for work conducted by his father.

In his defence, Skinner claimed he had been confused over the rules, and blamed a lack of information given to him by the European Parliament.

On 31 March 2016, Skinner was found guilty of: one count of making a false instrument; one count of fraud; and one count of false accounting. Warned that he would face a prison sentence, on 29 April 2016 he was jailed for 4 years.