The 62-year-old leaves the bank this week after 20 years, which included eight years as head of government relations before he became PA director in 1997.
In a pre-retirement move, MacThomas will join the Industry and Parliament Trust (IPT) - a non-lobbying charity that fosters understanding between parliament and business - as director of corporate development.
He will work on a four-day-a-week basis for an initial period of two years.
'I did not want to go from a full-time job to nothing and I am passionate about the need for parliament and business to work more closely together,' he said. 'With more and more MPs elected without much practical experience of business, the role of the IPT is becoming increasingly important.'
Barclays is seeking a replacement for MacThomas, who led its 13-strong PA team and reported to public policy director Mike Davis.
The bank is working closely with the Office of Fair Trading's Payment Systems Task Force, set up to address concerns that banks take too long to process transactions.
The Consumer Credit Card Act is also a major issue for Barclays' lobbyists.
Barclays was thrust into the heart of the debate over credit card companies' responsibility to consumers when then CEO Matt Barrett admitted in 2003 that he personally found credit cards too expensive.