[8][9] Players released at the end of their contracts included Joshua Bohui, 2020–21 top scorer Jevani Brown, Callum Coulter, Paris Cowan-Hall, Luke Gambin, Callum Harriott, Tom Lapslie, club captain Harry Pell, Courtney Senior, Omar Sowunmi and Diaz Wright.

[10] Colchester also announced their first signing of the season with Cole Skuse joining from Ipswich Town on a two-year deal following his release from the Suffolk club.

[18] Colchester re-signed Frank Nouble for a third time on 18 June when he joined on a free transfer from Plymouth Argyle on a two-year deal.

Joining alongside Nouble was Alan Judge who became the fourth player to sign for Colchester directly from Ipswich Town following his release.

[19] Wales under-21 defender Cameron Coxe joined Colchester on loan from National League side Solihull Moors on 2 July.

[20] On 5 July, Brendan Sarpong-Wiredu and Tommy Smith both extended their contracts with the club by a further year, with both now set to expire in summer 2023.

Three first-half goals from Son Heung-min, Lucas Moura and Dele Alli were enough to give the Premier League side victory as fans returned to the stadium for the first time in seven months.

Summer signing Alan Judge put the hosts 3–2 up against his former club, but a late equaliser from Wes Burns ensured the game finished a draw.

[28] On 2 August, Peterborough United signed midfielder Kwame Poku from Colchester for a "substantial six-figure fee" on a four-year contract.

[33] On 12 August, young defender Billy Cracknell joined National League South side Concord Rangers on loan until January 2022.

Jon Guthrie's first-half goal won the match for the visitors, but they did have their captain Fraser Horsfall sent off for deliberate handball in the 84th-minute.

[35] Ahead of their home match against Mansfield Town on 17 August, Colchester United announced the signing of Charlie Daniels on a one-year deal.

[36] In the match against Mansfield, Daniels made his debut from the substitutes' bench, the visitors struck first through former U's loanee Elliott Hewitt in the 72nd-minute.

However, Freddie Sears scored Colchester's first goal of the season in the fifth minute of added time from the penalty spot after Frank Nouble had been fouled.

[37] Freddie Sears converted his second consecutive penalty kick within the first ten minutes of Colchester's game against Oldham Athletic on 21 August.

[38] On 21 August, Harvey Sayer joined National League South side Billericay Town in a three-month loan deal.

[43] Harry Beadle, Armando Dobra, and Jake Turner all made their club debuts in Colchester's 1–0 home defeat by Gillingham in the EFL Trophy on 7 September.

Colchester were level ten minutes later when Alan Judge scored his first goal for the club, tapping in Freddie Sears' low cross.

[51] Colchester secured a late draw at home to Bristol Rovers on 19 October with Noah Chilvers scoring an 88th-minute equaliser after Brett Pitman's second-half opener.

Junior Tchamadeu received his first career red card alongside Rovers' Trevor Clarke for violent conduct in the first minute of stoppage time.

This followed Cian Harries' dismissal four minutes earlier for a second bookable offence, meaning Rovers finished the match with nine players.

[5] Jake Hutchinson joined National League South side Tonbridge Angels in a month-long loan deal on 26 October.

[2] On 30 October, Colchester signed Shawn McCoulsky from Forest Green Rovers on a short-term contract having been released from the club in the summer.

[4] The U's drew 0–0 with Ipswich Town on 9 November in their third and final EFL Trophy group match and lost 4–3 following a penalty shoot-out.

[60] On 26 November, defender Billy Cracknell signed for Isthmian League Premier Division side Bishop's Stortford in a month-long loan deal.

The visitors took the lead through Dom Telford after 36-minutes but Freddie Sears' eighth goal of the campaign with 78-minutes played ensured a point for both teams.

On 30 November, Colchester played Swindon Town in the Southern Section Round 2 of the EFL Trophy away from home where the U's beat them 1–2.