Portstewart took another stride forward in 1979, when they applied to join the Northern Ireland Intermediate League (NIIL).

Portstewart created history in 1994, when they defeated Limavady Utd 1–0 in the William Youngers Intermediate Cup final, becoming the first junior team in over 100 years of the competition to lift the trophy.

Moffatt's decision to step down as manager resulted in his assistant Trevor McKendry taking charge of team affairs, and under his leadership Portstewart continued to grow.

McKendry led the team to the North West Cup final in 2004 when they were narrowly defeated by Tobermore United.

In the 2005/06 season, when Portstewart gained promotion to second tier of Irish League football for the first time in the club's history.

During the 2018/19 season, a match between Portstewart and Sport & Leisure Swifts was abandoned after 70 minutes when a fan joined a "mass brawl" between players and coaches.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.