This run of form cost manager Steve Ball his job in February, while his interim replacement Wayne Brown fared little better.

Hayden Mullins was promoted to interim head coach on 31 March and a number of wins, including victory against bitter relegation rivals Southend United, aided Colchester to safety in the penultimate game of the season.

Colchester were eliminated in the first round of the FA Cup in a penalty shoot-out to Northern Premier League Division One North West side Marine.

A brace from Dan Butler and one from Siriki Dembélé all but secured victory for Peterborough, before Colchester scored their first goal of pre-season when Jevani Brown earned an 81st-minute consolation.

[20] Colchester played their first competitive match of the season in the first round of the EFL Cup on 5 September when they faced Championship side Reading.

Debuts were handed to Tommy Smith and Miquel Scarlett in defence, and Jevani Brown made a return to the Colchester first-team following his loan spell last season at Forest Green Rovers.

[22] On 9 September, young forward Michael Fernandes signed for National League South side Dartford on loan until January.

Ten minutes later, the U's were two ahead when Callum Harriott doubled their lead from the penalty spot after Conor McAleny's handball offence.

McAleny made amends in the second-half, scoring from a penalty kick after Cohen Bramall was deemed to have fouled Dylan Bahamboula.

[31] On 9 October, Colchester announced the signing of former Manchester United Academy forward Joshua Bohui, who had his contract cancelled at Dutch side NAC Breda earlier in the week.

Callum Harriott's second goal in as many games had given the U's a first-half lead, but Walsall struck back in the second-half through Elijah Adebayo to draw 1–1.

[34] Ollie Kensdale was loaned out to National League South side Braintree Town, making his debut for the club on 10 October.

[43] Colchester were knocked out of the FA Cup first round by Northern Premier League Division One North West side Marine on 7 November.

Nicky Maynard had opened the scoring for the hosts mid-way through the second-half, but Luke Norris' third goal of the season on 85-minutes secured a point for the visitors.

Luke Hendrie equalised for the visitors mid-way through the second-half, but Callum Harriott scored his second goal in as many games to secure victory for the U's.

[53] On 15 December, Colchester were beaten 2–1 at Cambridge United in front of almost 2,000 fans, but the match was overshadowed by a small number of the home supporters booing when players took the knee before kick-off.

[54] On 18 December, the Football Association announced no further action would be taken against Colchester after fans had booed players taking a knee in the home win against Grimsby.

[4] On 21 December, Marley Marshall-Miranda, who had made his first-team debut earlier in the season, signed a new two-and-a-half-year contract to keep him with the club until summer 2023.

[56] In their Boxing Day Essex Derby match against Southend United, Colchester were beaten 2–0, with two first-half goals from Simeon Akinola and Timothée Dieng.

[58] Colchester's first scheduled game of 2021 was postponed on the morning of the fixture with Tranmere Rovers due to players in both squads showing symptoms of COVID-19.

[64] Luke Gambin departed Colchester on 20 January to join fellow League Two club Newport County on loan until the end of the campaign.

[68] On transfer deadline day, Colchester re-signed Frank Nouble on loan from Plymouth Argyle until the end of the season, while 2019 Charlton Athletic loanee Brendan Sarpong-Wiredu joined the club on a permanent basis.

[69] Cohen Bramall left the club to join League One side Lincoln City for an undisclosed fee, while incoming loan signing Josh Doherty from Crawley Town was a direct replacement.

James Perch put Mansfield back in front with nine minutes remaining, but Frank Nouble scored his first goal of his loan spell to rescue a point for Colchester in the 89th-minute.

[79] Another dreadful display followed on 9 March as Colchester were humbled 3–0 at Harrogate Town, failing to score away from home once again with the U's not recording a goal in 10 hours and 35 minutes.

[82] A 1–0 home defeat to fellow strugglers Port Vale on 20 March dropped Colchester to 22nd in the League Two table, just seven points clear of the relegation places.

However, Tranmere pulled a goal back from the penalty spot seven minutes later after Tommy Smith was judged to have handled the ball in the area.

[3] On 1 April, former Exeter City, Milton Keynes Dons and Bristol Rovers manager Paul Tisdale joined the club in an advisory role alongside Mullins until the end of the season.

In the fourth minute of first-half injury time, Ryan Clampin's volleyed strike handed the U's the lead, and they held on in the second half for the three points.

Josh Bohui scored his first goal in English football from the substitutes bench to ensure that the U's would finish the season no lower than 22nd in the table.