Having narrowly avoided relegation to League Two on the final day of the previous season, manager Joe Dunne began strengthening the team early in pre-season, announcing former Arsenal loanee Craig Eastmond had signed a pre-contract agreement with the club on 20 May.

[9] Long-serving defender John White decided to bring an end to his nine-year stay with Colchester after rejecting a reduced-terms contract offer by the club.

Ben Newson had given the home side a first-half lead prior to Craig Eastmond being stretchered off following a challenge from Ryan Doyle.

[14] On 12 July, Colchester faced AFC Sudbury and secured a 5–0 win with a brace from Sammie Szmodics and goals from triallist Phil Roberts, Marcus Bean and John-Joe O'Toole.

[20] The following day, the U's faced Braintree Town at Cressing Road where they won 4–1 with goals from Andy Bond, Marcus Bean, Freddie Ladapo and Ryan Melaugh.

[22] John-Joe O'Toole made a move to Bristol Rovers for an undisclosed fee on 24 July having previously spent time on loan there during the 2012–13 season.

[29] The U's bounced back from midweek Cup disappointment to record a second successive 1–0 league victory over Port Vale with Gavin Massey scoring the decisive goal.

Freddie Sears had opened the scoring following a counter-attack in the 25th minute, but the Blades equalised on the stroke of half-time when a Harry Maguire shot slipped through Sam Walker's gloves.

Having failed to make a first-team appearance in the first month of the season, both the club and player agreed to mutually cancel Izzet's contract in order for him to find regular football.

However, Magnus Okuonghae was sent off for a second bookable offence in the 52nd-minute as former Colchester youth team product Medy Elito scored an equaliser one minute later.

The game was played at Northampton Town's Sixfields Stadium due to an ongoing dispute between the club and the Ricoh Arena's.

It ended 2–0 to the "home" team and Joe Dunne said that he had "no complaints" with the result considering he only had nine players available for training on the Thursday prior to the game.

Incoming were winger Jeffrey Monakana from Preston North End,[38] and full back Luke Garbutt from Everton as cover for Ryan Dickson who had been suffering from a virus in recent weeks.

[40] Following Pappoe's red card, further defensive reinforcement was required as Dunne recruited Queens Park Rangers' Northern Ireland under-21 international Jamie Sendles-White and Bradford's Matt Taylor on one-month loan deals.

[42] Matt Taylor scored in just his second appearance for the club in their 1–1 draw with Bristol City at Ashton Gate Stadium on 28 September, a game which saw the debut of Academy graduate Sammie Szmodics who came on as a late substitute for Craig Eastmond.

[43] Colchester hosted promotion-favourites Wolverhampton Wanderers on 5 October as a team featuring a number of emergency loanees and youth-team products were beaten 3–0.

[47] Making his home debut on his birthday on 26 October, Macauley Bonne scored his first professional goal against Peterborough United eight minutes after coming on as a substitute for Clinton Morrison to end the U's winless streak with a 1–0 victory.

Kieran Agard gave the hosts the lead on 22-minutes, but Elliot Lee scored an equaliser, his first in professional football, in second half injury time.

[50] Colchester resumed League One activities on 16 November at home to Swindon Town and lost 2–1 with a Magnus Okuonghae goal their consolation as it left the U's with one win in 16 games in all competitions.

[53] They then travelled to Birkenhead to take on Tranmere Rovers on 30 November where they were beaten 2–1 with two goals for Ryan Lowe securing victory for the home side and Clinton Morrison scored his first of the season in stoppage time.

[54] Following a two-week break for the FA Cup second round in which Colchester did not take part, the U's faced bottom of the table Notts County at the Community Stadium on 14 December.

[56] On Boxing Day, Joe Dunne enjoyed his biggest win as Colchester manager when the U's beat Stevenage 4–0 at home.

After taking the lead through a deflected Luke Garbutt free kick, Crewe pulled two goals back in three second-half minutes to consign Colchester to a 2–1 defeat.

[65] Colchester won 4–2 at Brunton Park against Carlisle United on 18 January to move back into the top-half of the League One table.

[67] The January transfer window also saw the departure of youth-team graduate Freddie Ladapo, who left for Conference club Kidderminster Harriers.

[68] Colchester additionally signed Leicester City under-21 captain Alie Sesay on loan until the end of the season to provide cover for Magnus Okuonghae and Tom Eastman.

Luke Freeman pulled a goal back in the 89th minute for the home side but they then had Filipe Morais sent off for fighting in stoppage time.

[89] A 1–0 defeat to Oldham on Good Friday put the U's firmly back in the relegation picture, leaving them two points outside of the drop zone.

[91] On 26 April, Colchester effectively sealed their League One status for another season by beating already-promoted Brentford 4–1 in an impressive performance at the Community Stadium.

[92][93] In their final game of the season, the U's travelled to Walsall and secured a 1–0 victory after James Chambers' attempted clearance struck Craig Eastmond and flew into the net.