1990–1995

The following season, the Cheetahs were moved to the Southern Conference of the BNGL's Premier Division, but they struggled once again, finishing bottom of the four-team group with just two wins out of ten.^[7]

This resulted in the Cheetahs being relegated to Division One, where they were assigned to the East Midlands Conference. They moved home once again, playing their games at Newlands Park College in Chalfont St. Giles.^[8] They began the season with two ties away from home, before narrowly losing their first home game against the Stratford Tempests due to a last minute field goal.^[8] Two further defeats were followed by three successive victories, with the Cheetahs eventually finishing fourth in the group.^[9] 1992 saw them winning six of their games, again narrowly missing out on a playoff spot.^[10]

Their first real success came in 1993. After appointing a pair of new coaches, the team won all but one of their games to win the First Division South Central Conference, claiming their first ever conference title and qualifying for the playoffs.^[11] They were drawn at home to the Weymouth Renegades, whom they beat 15–8 with their three running backs each getting over 100 yards.^[8] In the quarter-final, they travelled to the Hereford Chargers—after conceding 22 points in the first quarter, they were unable to recover and ended up losing 15–22.^[8]

The following year, the Cheetahs switched over to the newly formed British American Football Association (BAFA) league. They were assigned to the Division 3 Midlands Conference, which also contained the Cambridge Cats, Colchester Gladiators and Norwich Devils, with their home games against the Gladiators and Devils being their only two wins that season.^[12] The following season also saw them struggle, with two of their three wins coming as the result of the London Mets forfeiting their games.^[13]

1996–1997

1996 saw the Chiltern Cheetahs celebrating their tenth anniversary with a friendly match against the visiting Hamlen Dragons—the Cheetahs defeated their German opponents 60–0.^[13] The team were moved to the newly formed British Senior League, where they played in the Division 3 Midlands Conference. Although they finished the season with five wins and five defeats, they recorded a number of individual records—quarterback Rob Suttling became the first Cheetahs player to pass for more than 1,000 yards in a season, and safety Jay Rayner recorded nine interceptions, the highest total in Division Three.^[13] The following year was one of their most successful. After a good start followed by three consecutive defeats, a run of five wins saw the Cheetahs finishing second in their group and qualifying for the playoffs for only the second time in their history. An away win against the Leicester Huntsmen was followed by a 26–16 home win over the Yorkshire Rams in the semi-final, a result secured by two interception touchdowns.^[13] The team then travelled to play the Division 2 playoff final at the Saffron Lane stadium in Leicester against the Bristol Aztecs, a team who had only conceded 32 points all season, with the Aztecs winning 6–27.^[14]

Compared with 1997, the next few seasons were unremarkable with The Cheetahs generally finishing in mid-table.

2004–2005

It wasn't until 2004 that they again experienced success, when they finished top of Division 2 South East with ten wins out of ten. This meant they finished at top seeds in the entire division, and so were assured of home draws. A 30–6 win over the South Wales Warriors in the quarter-final was followed by a 34–6 semi-final win over the Sussex Thunder. This set up their second playoff final, this time played at the Don Valley Stadium in Sheffield in front of 1440 spectators. They did not finish the season with another win, losing 16–32 to the Doncaster Mustangs.^[15]

Despite losing the final, the Cheetahs were promoted to Division 1A of the British American Football League. After winning their first match against the Southern Sundevils, they struggled at this higher level and only managed to win one more of their games, ultimately finishing third out of four teams in their group.^[16] This was still to gain a wild-card slot in the playoffs and they made the most of this opportunity, defeating the Staffordshire Surge and the London Blitz to gain a place in the final for the second successive season. As with their first playoff final eight years before, they played the Bristol Aztecs and lost only by a single touchdown.^[17]

2006–2007

They didn't recover from this and lost all ten games in the following season, only managing to score 32 points.^[18] They were therefore relegated back to Division 2, where they played the 2007 season in the South East Conference at their new home in Watford. They continued to struggle, winning only two of their ten games.^[19]

2010

2010 was an eventful year for the Cheetahs. Drew Anderson was appointed as head coach, numerous adjustments and new arrivals made it a busy off season, including the Cheetahs being transferred to the BAFACL Division 2 West. The pre-season began with two scrimmage games v. London Blitz and Cambridgeshire Cats. They began the 2010 League campaign 3–0 with consecutive wins away from home including a thrilling 27–14 win against the Cornish Sharks. Three consecutive defeats then followed, twice against the Berkshire Renegades and an unfortunate defeat away to Hampshire Thrashers, which made the Cheetahs 3–3. Two thrilling come-from-behind home wins v. Gloucester Banshees and runaway divisional leaders Hampshire Thrashers, which gave the Cheetahs a chance of sneaking into the playoffs. A devastating 35–13 loss at home to Milton Keynes City Pathfinders put paid to any Cheetahs playoff hopes and the season ended with another home defeat to Cornish Sharks. The Cheetahs finished the season 5–5 and 3rd position in the division.

2011

2011 was another eventful season for the Cheetahs, the club celebrating their 25th anniversary, with more several comings and goings in the playing roster and coaching staff. Linebacker Jamie Brown was installed as the team's new defensive co-ordinator and a partnership on offense between retired kicker Douglas Andrews and quarterback Martin Brown, after the departure of previous coach Adrian Stemp. Brown became the team's new starting QB ahead of the established Paul Symonds, who took the opportunity of also playing wide receiver as well as quarterback after recovering from an arm injury sustained the season before. Backup quarterback Nik Maxey, who once played for the Great Britain Crusaders (Under 18) and Bulldogs (University) teams, would also take a more active coaching role as the 2011 season unfolded. Head coach Drew Anderson announced toward the end of the season that he would step down to become the head of BAFA's Community Football scheme.

Before the 2011 season kicked off, Cheetahs formed a partnership with the University of Hertfordshire Hurricanes team, culminating in two scrimmage games to help prepare the Hurricanes for their winter football season. So successful were the games that several players, led by former Cheetahs linebacker Richard Ward, returned and he brought a few Hurricanes players with him to play for the Cheetahs in the 2011 season.

The club also announced that they would form a Youth Kitted team with help from the local youth and community authority.

Before the season kicked off proper in April, the Cheetahs were transferred back to the Eastern Conference of BAFA's Community League to be reunited with their old rivals from Kent, Norwich, Bedfordhire, Essex and Milton Keynes, who themselves spent a season with the Cheetahs in the West Conference joined them back in the East.

The season began with the team away from home against the Bedfordshire Blue Raiders in which the Cheetahs shut out their Bedford-based rivals 15–0. Another shut-out in the following game, which would be the team's 25th Anniversary Game at home v a severely depleted Norwich Devils with the Cheetahs thumping the Devils 37–0. The Devils announced shortly after that they could not continue playing for the remainder of the season which meant the Cheetahs had an extra win under their belts, albeit by default. A history-making third shut-out in succession happened in the next game away in Kent against the Maidstone Pumas. The Cheetahs destroying their opponents 61–0. This made the Cheetahs 4–0 for zero points conceded, ahead of what would be the most testing time of the Cheetahs' season.

The Cheetahs themselves would suffer a shut-out themselves in the following game away against the Kent Exiles. The Cheetahs, failing to move the ball effectively at a drizzle-soaked Crockenhill suffered an 18–0 loss in what was the Conference-topping game. A bruising 31–20 loss against a physical and much improved Milton Keynes City Pathfinders team pushed the team further out of the Playoff picture with the season record standing at 4–2.

The following game, the Cheetahs bounced back at home at a sweltering Fullerians with temperatures well in the 80s against the table-topping Essex Spartans in which the Cheetahs ran out 19–6 winners. A close, and unfortunate defeat away at Milton Keynes by 20–16 would ultimately crush the Cheetahs' post-season Playoff hopes. The Cheetahs exacted revenge against the Exiles in the return-game at home by 23–14 which saw the game suspended temporarily in the 4th quarter by a brief thunderstorm. The final home game then saw the Cheetahs thump Bedfordshire by 43–6. The Cheetahs finished the 2011 season with their first winning season since their 10–0 season in 2004 with a record of 7 wins for 3 losses and 0 ties, and the fourth lowest points-conceded in the entire division.