Ashley Mote, 79, denied 11 charges relating to fraudulent claims to pay people he said were "whistleblowers".
The offences included obtaining a money transfer by deception, fraud, acquiring criminal property and false accounting.
Mote, from Binsted, Hampshire, sat as an independent MEP for South East England from 2004-2009 after being expelled from UKIP for benefit fraud.
He was found guilty of four counts of obtaining a money transfer by deception, three of false accounting, two of fraud, and one each of acquiring criminal property, concealing criminal property and theft.
The offences took place between November 2004 and July 2010.
Mote was released on conditional bail. However, Mr Justice Stuart Smith at Southwark Crown Court said there was a "very strong likelihood" a custodial sentence would follow.
The jury heard how Mote submitted numerous false expenses claims for payment for work that organisations had allegedly carried out on his behalf.
Mote claimed the money was to pay whistleblowers in cash through third parties. He also said he had been "targeted for being an anti-EU MEP."
During his time an MEP he also made £250,000 legitimate expenses claims.
No date has been set for the sentencing.
A former MEP has been convicted of fraudulently claiming almost £500,000 in European Parliament expenses.