Ashley Mote, 79, was convicted of 12 charges relating to fraudulent claims to pay people he said were "whistleblowers".
The offences included fraud, acquiring criminal property and false accounting.
Mote, who sat as a UKIP and then independent MEP for South East England, was sentenced to five years at London's Southwark Crown Court.
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A former MEP who fraudulently claiming almost £500,000 in European Parliament expenses has been jailed.