Both founding clubs had a strong history of their own, achieving numerous cup victories in the respected Portsmouth Dockyard League and Meon Valley League.

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The newly formed Baffins Milton Rovers began their journey in the Portsmouth Saturday League Premier Division and immediately tasted success, lifting the division trophy in their inaugural 2011/12 season. This early triumph set the stage for further progress, and at the end of the 2012/13 campaign, the club achieved promotion to the Hampshire League after finishing as runners-up to Waterlooville Social Club.

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The 2013/14 season proved to be a historic one for Baffins Milton Rovers, as the club achieved an impressive treble. They clinched the Hampshire League Premier Division trophy, triumphed in the Hampshire League Cup with a decisive 4-0 victory over Colden Common, and celebrated victory in the Portsmouth Senior Cup after defeating local rivals Moneyfields at the iconic Fratton Park.

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In 2015, a significant step forward for the club's infrastructure was taken with the acquisition of a 50-year lease from Portsmouth City Council for the northern section of Langstone Harbour Sports Ground. This allowed for crucial developments, including the construction of a 120-seater stand, changing rooms, a perimeter fence, and concrete hardstanding. The upgraded ground was officially opened with a friendly match against Salisbury on August 3rd, 2016.

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Continuing their on-field success, Baffins Milton Rovers finished as runners-up in the Hampshire League Premier Division in the following season. However, the 2015/16 campaign saw them go one better, winning the Hampshire League Premier Division title in dominant fashion, losing only three matches throughout the season. The club also lifted the Portsmouth Senior Cup for the second and final time with a 3-1 victory over Havant & Waterlooville's Southdowns College Team in the final.

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The 2016/17 season marked a new chapter in the club's history as Baffins Milton Rovers made their debut at Wessex League level. Stadium upgrades facilitated the club's acceptance into step-six of the non-league pyramid. Their first season in the Wessex League was a resounding success, finishing as runners-up to Hamble Club and achieving promotion to the top flight of the Wessex League (Wessex Premier Division). The season concluded with an appearance in the Wessex League Cup final, where they finished as runners-up to Sholing.

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Baffins Milton Rovers have now completed five seasons at step-five level (Wessex Premier Division). The 2018/19 campaign saw the club reach their furthest ever round in the FA Vase, eventually losing to Cray Valley Paper Mills in the Fourth Round Proper. To cap off a memorable year, Baffins Milton Rovers won the Wessex League Cup with a 1-0 victory over Portland United at AFC Portchester's Wicor Recreation Ground.

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Ahead of the 2022/23 Wessex Premier Division campaign, the club appointed former assistant manager Danny Thompson as the first-team manager. Thompson's first season in charge proved successful, with the club lifting the League Cup trophy, once again defeating Petersfield Town at Wicor Recreation Ground, home of AFC Portchester.

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The 2023/24 season witnessed Baffins Milton Rovers achieve their best-ever league finish, clinching fifth place and the final play-off spot on the last day of the season with a 3-1 victory away at Christchurch. While their play-off journey ended with a narrow defeat to eventual runners-up AFC Stoneham, it marked a significant milestone in the club's continued progress.

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The following campaign saw the club record their best-ever run in the Emirates FA Cup, reaching the First Qualifying Round. Their cup journey came to an end with a 4-1 defeat away at Southern Premier Division side Plymouth Parkway. 2024/25 also saw a change in management, with Thompson stepping down as manager, following a defeat at Christchurch. Assistant manager Matt Jones subsequently took charge as Interim Manager for the final 16 matches of the campaign, guiding the club through a period of transition, and only missed out on the play-offs on the final day of the season.