Frank's teams were known for long Scottish Junior Cup runs with the furthest being a Quarter Final replay loss in extra time to eventual winners Arthurlie in 1997–98.

The club then appointed former player Neil Muggins as manager and after an unsuccessful season he left and was replaced by Sandy McLean.

Brian Stevenson came in as manager and steered the club to a 3rd-place finish and Beith qualified for the West of Scotland Super League 1st division after beating Dalry Thistle in a two legged play off with the season ending with a North Ayrshire Cup Final loss to Kilbirnie at Largs.

In 2008–09, the club won the West of Scotland Cup, beating Auchinleck Talbot 2–1 in the final at Pollok and after leading the league for a long period fell away and finished 3rd.

In 2009–10 the following season they won the West Premier title by a then record number of points only losing one game, meaning they qualified for the senior Scottish Cup.

During the 2010–11 season, Beith entered the Scottish Cup at the first round stage after qualifying as champions of the West of Scotland Super League Premier Division.

In the third round they faced Second Division Airdrie United and led 2–0 with ten minutes remaining of the tie at the Excelsior Stadium, before full-back Marc McShane was red carded.

John Millar then came back re-invigorated and got some good results but unfortunately with suspensions and injuries taking their toll lost the last game away to Shotts to be relegated.

Following an inconsistent start to the season no doubt due to the large turnover in the playing staff and then the club won the Scottish Junior Cup for the first time in 2015–16, defeating Pollok on penalties after a 1–1 draw.

During the 2018–19, Beith Juniors progressed through two preliminary rounds and the 1st and 2nd round proper to play against Championship leaders at the time, Ayr United making this the first all Ayrshire Junior and Senior Scottish Cup tie, Beith holding the Honest Men for 62 minutes before conceding then losing two goals in the last five minutes after trying to chase a result to lose 3–0.

[3][4][5] As of 5 December 2024[6] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.