Following his tenure at the Manchester United bench, McGuinness had a four-year stay in Greece, leading Panachaiki through their first appearance in a European competition, the 1973–74 UEFA Cup.

McGuinness continued to be involved at Manchester United after the end of his playing career, getting heavily involved in coaching, and in 1964, he replaced Jimmy Murphy as reserve team manager, as Murphy left that role after managing the reserve team to a sixth FA Youth Cup triumph.

McGuinness was sacked in December 1970, after a dramatic comeback which saw United draw 4–4 with Derby County in a league fixture at the Baseball Ground.

Under McGuinness, Aris finished fourth in the 1971–72 Alpha Ethniki season, and ninth a year later, albeit being tied with three teams in sixth position.

He took over Panachaiki in 1973, finishing sixth in the Alpha Ethniki his first year while advancing to the UEFA Cup second round in the team's first ever European campaign.