With the likes of Colin Hawkins and Ken Oman in his way of regular first team football, he joined rivals Shamrock Rovers and spent 2 seasons scoring 7 goals in 57 total appearances there where he established himself at the heart of their defence before re-joining Bohs in time for the 2006 season.
Despite putting in a superb performance in the Setanta Sports Cup Final,[4] Jason and Bohemians had a disappointing 2010 season where the club lost their league title on goal difference and failed to make an impact in Europe where they made an embarrassing exit to Welsh side The New Saints.
[5] He scored against FC Spartak Trnava in the 2012–13 UEFA Europa League[6] McGuinness signed once again for The Hoops in November 2012.
[7] McGuiness signed for another of the big 4 Dublin clubs, St Patrick's Athletic, on 11 November 2014[8] before being released in June 2016.
The day after his release, it was announced McGuinness had joined the NIFL Premiership with Cliftonville where he scored against AEK Larnaca FC in the 2016–17 UEFA Europa League[9]