Some SoSFL clubs opted to join the EoSFL, including Annan Athletic before they were elected to the SFL in 2008.

Dalbeattie Star and Threave Rovers also joined however both subsequently left to rejoin the SoSFL and then later the Lowland League.

This left the league with an uneven number of clubs, and they were expected to fill the vacancy in the summer of 2005, with Gala Rovers widely touted as likely candidates.

The only change that happened at that year's AGM of the league, was that Tollcross United announced that they would be competing as Tynecastle from the 2005–06 season.

At the 2007 AGM, agreement was reached to admit the reserve side of Berwick Rangers as the twelfth member of the First Division.

However, the reserves lasted only one season following Berwick Rangers' relegation to the fourth tier of Scottish football.

They initially had to play home matches in the nearby town of Annan, the club that took their place in the SFL.

The admission of Duns prior to the 2011–12 season, and then Burntisland Shipyard in 2012–13 brought the number of sides in the EoSFL to 26, the highest it had ever been up to that point.

Beginning in 2017 the league experienced a resurgence with SJFA East Superleague champions Kelty Hearts joining from the Juniors.

The EoSFL's two-tier format, which began in 1987–88, was abolished for the 2015–16 season due to dwindling numbers and replaced with a single division.

Due to the COVID-19 pandemic, no relegation took place in 2020 meaning the Premier Division was temporarily increased to 18 clubs.