Potton Colts Football Club originally existed during the 1940s and was resurrected in 1980 by Martin Emery and John Jakes who formed a team at the under 12 age group and which played its matches at the old Recreation Ground on Sandy Road. In 1984 a prefabricated building was donated by local company Potton Timber to provide changing rooms and storage facilities. Facilities were further improved when a number of parents installed floodlights to allow the teams to train during the evenings.

Potton Colts consisted of just two or three teams until the mid 1990s when it began to expand and by the start of the 1999-2000 season it had a team at each age group from under 10 to under 16. In 1999 the Club established its first ever mini-soccer team at the under 10 age group and entry into that format proved to be a big success and ensured that the Club continued to grow in the new millennium. In 2003 a team was formed at the under 7 age group and in 2004 the Club experimented with providing football for the over 16s. This proved to be so successful that two teams were set up at under 17 and under 18 to meet the demand for the next two seasons.

Girls football was not ignored and with a few girls having played in the under 10 teams the Club formed it's first ever girls team in 2003 at the under 12 age group. This proved to be a very popular decision and a second girls team was formed in the following season with both sides playing mini-soccer in the Chiltern Junior Seven league. In 2006 the girls section expanded and the club became the first in the County to form a girls under 18 team with 18 players registering in its first season.

In the late 1980s the Club started to organise it's own annual 5-a-side tournament. The tournament became very popular with a reputation for its friendly atmosphere and it expanded in the early 90s to become the biggest in the area and is now run over two days on a weekend in June or July each year. In 2004 a girls competition was included and in 2006 under 8 and under 9 age groups were inluded for the first time.

In 1991 the first steps were made to begin a relationship with Potton United FC and the, then, new under 11 team played Potton Colts' first match under floodlights on United's pitch, an exciting encounter which saw Potton come back from three goals down to draw three-all. That started a trend which still continues every season with a few of the Potton Colts' teams playing floodlit challenge matches every season. Since 1994 Colts have provided many players for United's reserve side and in the 2005/2006 season all but one of the squad were former Colts players. Since 1994 some 24 Colts players have progressed to play for the senior club's first team in the United Counties League. Since 1999 United have made their ground available for the oldest of the Potton Colts teams to use for their home matches.

In 2002 Graeme 'Curly' Barham arranged for the under 10 - 15 teams to play friendly matches against the Arsenal FC Soccer School teams during their summer residential course at Shuttleworth College. This has taken place every year since and led to Colts' players attending match day visits (including a training session) to the Arsenal football stadium every season and, in October 2005, Arsenal brought their soccer school to Potton.

During 2003 the Club's 'Constitution' was changed, 'Codes of Conduct' were introduced and managers and coaches were put through Football Association training courses. This enabled the Club to be awarded Chartered Status just before Christmas 2003. In 2004 the Club was surprised to win the Bedfordshire County FA award for Best Chartered Standard Club. In 2005 the Club not only won the county award again but also won the East of England regional award for Best Chartered Standard Club.

In 2003 Potton Colts moved from the Sandy Road ground to the new Recreation Ground in Mill Lane. This new facility was provided by the Potton Charities and boasts very modern changing rooms for teams and referees complete with showers, catering and storage facilities. The playing surface is large enough to support two 11-a-side adult sized pitches and one mini-soccer pitch and is considered by many visitors to be one of the best venues in the region for youth football.

In the 2004-05 season the Club helped raise funds for a number of charities including taking part in the national 'Kick For Clic' cancer charity campaign for which the Club raised over £360 with a penalty competition at its annual 5-a-side tournament. Also, thanks to Anne Tredget, the Club arranged its own version of the 'Kit for Africa' campaign and donated a complete set of football kit plus over thirty pairs of football boots for the children of the Nyamahasa Primary School near Masandi in Uganda.

The Club decided to continue its charity fund raising and in the 2005/06 season helped raise funds for the charity 'UK Diabetes' in rememberance of Derek Inskip, the former Potton United Club Secretary.

Over the years the Club's teams have had numerous successes competing in the many summer 5-a-side and other small-sided tournaments, probably the best performance being in 1996 when the Under 15s progressed to the last 16 of the National 6-a-side championships. Honours have been less forthcoming in the 11-a-side game and it was not until the 1994/95 season that teams began to win silverware in the Royston Crow Youth League and since then have been fortunate to win at least one trophy every season.

In recent times the Club's players have come to the attention of professional clubs. Former under 13/14 player Chris Ewles went on to sign for Cambridge United and established a professional career in the Football League. Thomas Beech also signed forms for Cambridge United and went on to to make many appearances for their youth and reserve teams. In 2005/06 Colts had several players attached to 'Football Academy' and 'School of Excellence' sections at Rushden & Diamonds, Watford and Leicester City.

The girls also gained individual recognition in 2005 with one under 14 player signing-on with the Rushden & Diamonds Academy and two players being selected for the under 12s Bedfordshire Elite squad.