Before the start of the 2018-19 season, a host of Junior clubs, including Musselburgh, moved across to the East of Scotland Football League to join the recently established Scottish Football Pyramid. This presented clubs the opportunity to potentially gain promotion to the SPFL creating an increase from 13 teams to 39. The clubs who made the move would subsequently be split into three parallel conferences. Musselburgh finished 3rd in the
2018–19 season as part of 'Conference A' under the management of Calvin Shand until January 2019, and then Kevin McDonald for the duration of the campaign. As a result, the club qualified for the newly established East of Scotland Premier League for the 2019-20 season, one tier below the
Lowland Football League. They also got to the East of Scotland League Cup final, but lost 1-0 to Bo'ness United at Montgomery Park. Due to the outbreak of the global COVID-19 pandemic, the
2019–20 season was suspended in March 2020 and then curtailed in April with a 'points per game' system adopted. This resulted in a 10th place finish for the Burgh. In
2020–21, the season was delayed until October with matches played behind closed doors and by January, the season was suspended. A vote was taken a few months later and in April the season was declared 'null and void', with Musselburgh in 4th place. At the start of the
2021–22 season Kevin Milne was appointed to replace the outgoing Kevin McDonald who joined the Kelty Hearts coaching staff. However, Milne quickly departed the club. Musselburgh then appointed Joe Hamill as manager from East Lothian rivals,
Haddington Athletic. The Burgh would finish in 8th place following a disappointing second half of the season and Hamill would resign the following September following a Scottish Cup defeat to
Newtongrange Star. Liam Burns took the reigns for the
2022–23 season, and at 27 years old became the youngest manager in the clubs history . He went on to steer the club to a 3rd place finish in the East of Scotland Premier League. In the following campaign
2023–24, the club would take one step further with a 2nd place finish behind eventual champions,
Broxburn Athletic. It would be third time lucky for Burns and the team as Musselburgh won the
2024–25 East of Scotland Premier League. They were crowned champions following a 4-0 away win at
Sauchie Juniors in the penultimate game of the season, with all four goals being scored by forward Jordan Smith. Musselburgh would go on to complete the East of Scotland double by winning the League Cup. They defeated
Kirkcaldy & Dysart 2-0 in the final at St. Albans Park, with Jordan Smith scoring both goals. In between these two successes, the club earned an opportunity at promotion to the Lowland League in a two-legged play-off against
West of Scotland Football League champions,
Clydebank. Musselburgh fell short losing the tie 3-1 on aggregate remaining in the East of Scotland Premier League. At the start of the
2025–26 season, it was confirmed there would be at least two automatic promotion places available to the Lowland League. The top two teams, with the potential for more, would gain entry to the newly established Lowland League East following the regionalisation of the fifth tier . Musselburgh endured a frustrating campaign with mixed results, which resulted in the departure of Liam Burns with only a handful of fixtures remaining . == Scottish Cup (2020-present) ==