In the fourth round, Colchester beat league rivals Crawley Town 3–1 to set up a trip to Old Trafford to take on Manchester United.

In the EFL Trophy, Colchester won their first group with wins over Gillingham and local rivals Ipswich Town, but were defeated in the second round by Stevenage.

These players included David Agboola, Aaron Barnes, George Brown, Ken Charles, Noah Chesmain, Chris Forino, Arjanit Krasniqi, Eoin McKeown, Paul Rooney, Decarrey Sheriff, Sam Warde and Will Wright.

[4][5] On 17 May, young midfielder Kwame Poku signed his first professional contract, joining United from Worthing following a successful trial at the end of the 2018–19 season.

[6] On 20 May, Colchester announced that all out of contract players had been offered new deals, except for forward Mikael Mandron, who was allowed to leave the club after two years and 95 appearances, and winger Ryan Gondoh, who had spent the end of last season on loan at Halifax Town.

[8] On 7 June, Colchester announced the signing of former Leicester City under-23 midfielder Sammie McLeod on a two-year contract, joining from Maldon & Tiptree to link up with the U's under-23 side.

[14] After making 141 appearances for the club, defender Frankie Kent left Colchester to sign for League One Peterborough United for an undisclosed fee on 22 June.

[22] Later the same day, the club announced the signing of Denmark youth international Matthew Weaire from Brighton & Hove Albion on a two-year contract.

[25] Colchester started their pre-season friendlies with a game at Isthmian League Premier Division side Bowers & Pitsea on 5 July where they ran out 2–0 winners.

[30] On 19 July, young winger Todd Miller left the club to join Premier League side Brighton & Hove Albion, with the U's expected to receive compensation for the teenager.

[33] On 23 July, Charlton Athletic won 2–1 with a late goal in the U's latest pre-season friendly after Luke Norris had handed the home side the lead early in the second half.

On the back of a goalless first half, both teams had a man sent off for violent conduct in the 62nd minute, with Cohen Bramall shown red for Colchester and Jerry Yates for Swindon.

A ninth minute Luke Norris penalty gave the U's a 1–0 lead going into the interval, but two Cambridge goals in the second half left Colchester to a 2–1 defeat.

Each of the following penalties were scored by their takers, and U's Academy product Noah Chilvers converted the decisive spot kick to send Colchester through to the third round and their first win in the League Cup against top-flight opponents since 1979.

[48] On 2 September, transfer deadline day, Colchester signed young Charlton Athletic midfielder Brendan Sarpong-Wiredu on loan until January, with injuries ruling out Tom Lapslie, Harry Pell and Diaz Wright, and with Brandon Comley and Luke Gambin on international duty.

[55] Colchester drew their biggest crowd of the season of 9,481 when they hosted Premier League side Tottenham Hotspur in the third round of the EFL Cup on 24 September.

[58] On 11 October, teenage defender Ollie Kensdale joined National League South side Bath City in a month-long loan deal.

[62] Colchester held league leaders Crewe Alexandra to a 0–0 draw at Gresty Road on 22 October, but had the chance to win the game from the penalty spot in the seventh minute of stoppage time.

In the second half, Colchester went ahead after Cohen Bramall's free kick hit the bar, struck Crawley goalkeeper Michael Luyambula and went in.

[67] Colchester suffered defeat in the FA Cup first round for the fourth consecutive season when they lost 2–0 to League One side Coventry City on 9 November.

Luke Norris scored his fifth league goal of the season to hand the visitors the lead, but in the second half, Dean Gerken fouled Reuben Reid in the penalty area and Conor Thomas converted to equalise.

[76] After falling behind by two goals in their League Two game at Scunthorpe United on 14 December, Colchester battled back in the second half to claim a 2–2 draw.

In the second half, Cohen Bramall registered his first goal in the English Football League with a well taken free kick seven minutes after the restart to seal the victory.

[79] In the early League Two kickoff on Boxing Day, Colchester beat Leyton Orient 3–1 at Brisbane Road to move up to fourth in the table.

[86] On 10 January, both Cameron James and Diaz Wright joined National League South side Welling United on loan for one month.

[92] On 25 January, midfielder Louis Dunne joined Southern League Premier Division South side Farnborough on loan until the end of February.

[96] On 5 February, the club announced the departure of Junior Ogedi-Uzokwe to Israeli Premier League side Hapoel Hadera on a permanent contract.

[106] On 27 April, two days after they were scheduled to have played their final game of the 2019–20 season, Colchester United became the first English Football League team to announce the release of first-team players in light of the COVID-19 pandemic.

Chairman Robbie Cowling announced that four first-team players, namely Brandon Comley, Ryan Jackson, Frank Nouble and club captain Luke Prosser, would not be offered new deals once their contracts expired at the end of June.

[110] In the play-off semi-final second leg on 22 June, Colchester were beaten 3–1 after extra time, with Exeter heading to the Wembley final with a 3–2 aggregate victory.