At a special general meeting held in March 2018, the club's members voted in favour of applying to join the senior East of Scotland Football League.

Prior to becoming an SFA member in 2019, Bonnyrigg qualified to enter the senior Scottish Cup by winning the East Superleague on four occasions.

Better results were achieved in 2012–13, losing to SFL Second Division side Brechin City in a third round replay after wins over Girvan and Stirling University.

They were drawn at home against the cup holders Hibernian, with the match moved to Tynecastle Stadium in Edinburgh to accommodate the expected number of spectators and the basic facilities at New Dundas Park.

[12] Entering in the Second round in 2020–21, Bonnyrigg would defeat fellow Lowland Leaguers Bo'ness United 5–2, with Lee Currie scoring a hat-trick of penalties within 10 minutes of each other.

[13] In the next round, the Rosey Posey would nearly have a cup upset for the ages, with another Currie penalty and a strong performance from keeper Mark Weir nearly knocking out Scottish Championship side Dundee before a late equaliser sent the game to extra time.

Currie again put Bonnyrigg ahead from the spot, but two goals by Dundee in the second half of extra time ended the club's dream.