The 2020–21 season was Colchester United's 84th season in their history and their fifth successive season competing in League Two. Along with competing in League Two, the club also participated in the FA Cup, EFL Cup and EFL Trophy.

Following a promising start to the campaign, Colchester had just one win between 12 December 2020 and 9 April 2021 without a win, propelling them towards the relegation positions. 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. They finished the season in 20th position, six points clear of the relegation zone.

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. The U's also lost in the first round of the EFL Cup to Championship club Reading. At the same time, they exited the EFL Trophy at the group stage following defeats to Portsmouth and West Ham United under-21s. Despite this, they did earn the largest cup Essex derby victory with a 6–1 win against Southend.

Season overview Pre-season Colchester's place in League Two for the 2020–21 season was confirmed on 22 June 2020 following a 3–2 aggregate defeat to Exeter City in the semi-final of the League Two play-offs.

Chairman Robbie Cowling had already announced on 27 April 2020 that four first-team players would be released at the end of their contracts on 30 June. These players included Brandon Comley, Ryan Jackson, Frank Nouble, and club captain Luke Prosser. Citing the COVID-19 pandemic, Cowling admitted under normal circumstances he "would have been determined to re-sign" the released players.

The following day, the club also released a list of twelve further players who would not be offered new deals on the expiry of their current contracts. These included Dean Ager, Callum Anderson, Jamal Campbell-Ryce, Louis Dunne, Chandler Hallett, Tyrique Hyde, Luke Ige, Tariq Issa, Cameron James, Callum Jones, Percy Kiangebeni, and Bailey Vose.

On 14 July, Cowling released a statement to announce that John McGreal had left the club after four years as head coach.

Ethan Ross left the club on 24 July to join League One side Lincoln City.

On 28 July, McGreal's former assistant Steve Ball was announced as his successor.

Colchester played their first pre-season friendly at home to Gillingham on 15 August. They suffered a 2–0 defeat with goals from Stuart O'Keefe and Connor Ogilvie.

On 18 August, Colchester hosted back-to-back friendlies against Ipswich Town, both of which were 75-minutes in length. Colchester lost 4–0 in the first match, with a brace from Aaron Drinan and goals from Gwion Edwards and Idris El Mizouni. In the second game, Colchester were beaten 1–0. Alan Judge's first-half goal proved to be the difference between the sides.

Again the U's hosted back-to-back friendlies, this time the visiting team were Peterborough United. 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. In the second game, a young U's side were defeated by a first-half Ricky-Jade Jones brace.

Following the friendly with Peterborough, Colchester announced the signing of Tommy Smith following his release from Sunderland. He agreed a two-year deal having featured in a number of pre-season friendly matches.

On 28 August, the U's announced their second signing of the summer, former Liverpool goalkeeper Shamal George. He agreed a two-year deal following a trial period.

Colchester fell behind to their National League opposition Wealdstone on 29 August. This followed a melee between the two sets of players which resulted in Wealdstone's Danny Green being sent off. Tom Eastman equalised in the 52nd-minute, and Jevani Brown secured a 2–1 victory ten minutes later.

On 3 September, Colchester announced Steve Ball's assistant would be former Watford coach Hayden Mullins.

On 4 September, Harry Pell was named as Colchester United's new club captain. His vice-captain was newly signed defender Tommy Smith.

Colchester made their third summer signing ahead of the new season with the capture of Fulham striker Martell Taylor-Crossdale. He arrived on a season-long loan from the Premier League club.

September 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. Brown then scored his first goal for the club in the 37th-minute to give the U's a 1–0 lead, but Reading pulled level with a goal in first-half injury time through Lucas João. He then went on to score two more goals in the second half to seal his hat-trick and send Colchester out of the Cup in the first round. Marley Marshall-Miranda also came on as a second-half substitute to make his professional debut.

Martell Taylor-Crossdale came on as a second-half substitute for his club debut in Colchester's 2–0 EFL Trophy defeat to Portsmouth on 8 September. Also making his debut in goal was Shamal George. Two quick-fire first-half goals from Marcus Harness were enough to secure victory for Pompey.

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

The league season opened with a trip to Valley Parade to face Bradford City on 12 September. The match ended a goalless draw.

Under-23s players Ollie Sims and Matt Weaire were sent out on loan for first-team experience on 18 September until January 2021. Sims joined Southern League Premier South side Farnborough, while centre back Weaire joined Southern League Premier Central side Leiston.

Colchester secured their first win of the season in only their third-ever league meeting with Bolton Wanderers on 19 September. In their first home match of the season, the U's took a first-half lead through Tom Eastman's 44th-minute goal, before doubling their advantage from Jevani Brown's second goal of the campaign after 71-minutes. Sammie McLeod came on as an 83rd-minute substitute to make his professional debut in the 2–0 victory.

The U's were held to a 1–1 draw in their visit to Barrow on 26 September. Noah Chilvers' first professional goal handed the visitors a 1–0 lead after 34-minutes, but the hosts drew level on 54-minutes through Mike Jones.

September ended with a third successive cup defeat of the season for the U's. West Ham United under-21s were 1–0 winners through a 61st-minute Conor Coventry goal. Left back Harvey Sayer made his debut from the substitutes bench during the match.

October On 3 October, Colchester hosted Oldham Athletic on match day four. Colchester took a 27th-minute lead through Ben Stevenson, who recorded his first goal of the season. 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. Then two minutes later, Oldham equalised through Carl Piergianni. Colchester retook the lead on 65-minutes from a Miles Welch-Hayes header, but Oldham again equalised in the 89th-minute, McAleny again the scorer.

Noah Chilvers signed a new three-year contract on 5 October to keep him at the club until summer 2023.

Defender Danny Collinge was sent out on loan to Isthmian League North Division side A.F.C. Sudbury on 8 October until January 2021.

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. He signed a two-year deal with the club, joining up with Jon De Souza, who he played under at the Brentford Academy.

Colchester were held to a third successive draw on 10 October. 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.

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

Colchester fell to their first defeat of the season on 17 October. Hosts Carlisle United took a 2–0 first-half lead before Luke Norris scored his first goal of the season a minute before the interval. It was 2–2 by the 52nd-minute, Norris converting a penalty kick. However, Carlisle nicked the win with an 81st-minute goal from Aaron Hayden.

Having been on loan at Dartford, Michael Fernandes joined Ollie Sims on loan at Farnborough on 20 October, signing with his former club until January 2021.

The U's returned to winning ways with a 1–0 victory over Forest Green Rovers on 20 October. Noah Chilvers' second-minute goal and second goal of the season was enough to secure the win.

On 24 October, Colchester beat Harrogate Town 2–1 in their first-ever league meeting. Callum Harriott scored his third goal of the season on 52-minutes, before Ben Stevenson followed up two minutes later to double the U's lead. Jon Stead pulled a goal back for the visitors on 61-minutes, but the hosts held on for victory.

Colchester suffered their second league defeat of the season on 27 October at top of the table Newport County. Scott Twine opened the scoring on 51-minutes, but substitute Jevani Brown scored an 89th-minute equaliser for the visitors. In the first minute of injury time, Newport scored their winner through Pádraig Amond.

On 27 October, it was announced that Scunthorpe United had eight players test positive for COVID-19, and their next three fixtures would be postponed, including their match against Colchester originally scheduled for 30 October.

November Colchester signed former Watford striker Michael Folivi on 2 November on a contract until the end of the season.

Colchester returned to winning ways on 3 November with a 3–1 home win against Stevenage. Jevani Brown scored an 11th-minute opener, before the visitors equalised from the penalty spot four minutes later following a Tommy Smith foul. After the break, Brown added a second in the 57th-minute, and completed his hat-trick in the 81st-minute.

Colchester were knocked out of the FA Cup first round by Northern Premier League Division One North West side Marine on 7 November. The eighth-tier visitors took a 22nd-minute lead through Anthony Miley, but captain Harry Pell brought the U's back into the tie with a 64th-minute equaliser. The resilient Mariners took the tie to extra time, and held out to a penalty shoot-out. Colchester and Marine converted all of their penalties until Josh Bohui stepped up to take United's fourth, which he put wide. Jay Devine scored the subsequent kick and put Marine through to the second round of the Cup for the first time since the 1992–93 season.