On 22 October 2013 he signed for Colchester United on a one-month youth loan. His only Colchester goal was scored on 2 November in an away draw against Rotherham United: in stoppage time in the second half, with Rotherham winning 2–1, Lee scored with a header which hit the bar and bounced over the line to make the final score 2–2. He returned to West Ham on 21 November after four appearances and one goal for Colchester United.
Loan to Southend United
On 31 October 2014 Lee joined Southend United on a three-month loan. Within hours of signing for Southend, Lee suffered a hamstring injury and returned to West Ham for treatment. On 5 November Lee was ruled out of playing for at least two months. His loan was cancelled on 6 November and he returned to West Ham United, his parent club.
Loan to Luton Town
On 19 February 2015, Lee joined Luton Town on loan for one month. Lee chose to wear the number 38 shirt in memory of his former teammate at West Ham, Dylan Tombides who also wore number 38. He scored on his debut for Luton two days later, four minutes after coming on as a substitute for Andy Drury in a 3–2 defeat away to AFC Wimbledon. On 24 March 2015, Lee scored twice in a 2–3 home defeat by Wycombe Wanderers. On scoring he revealed a T-shirt showing a picture of Tombides, to whom he dedicated his goals. The following day his loan contract with Luton was extended until the end of the 2014–15 season. Luton manager John Still said of Lee "Elliot's been fantastic for us and we're thrilled to have him for the rest of this season."
Return to West Ham
Lee scored another hat-trick for the development squad when they faced Conference Premier club Woking in a pre-season friendly on 5 August 2014. Lee was an unused substitute in the League Cuppenalty shoot-out defeat by Sheffield United in the second round on 26 August 2014. He was given the number 36 for the first team the same day. On his first start for West Ham, on 9 July 2015, Lee scored his first goal for the club. In a Europa League first qualifying round match away against FC Lusitanos of Andorra, he scored the only goal from a cross from Matt Jarvis.
Loan to Blackpool
On 26 November 2015, Lee was loaned to League One club Blackpool until 3 January 2016. He made his debut two days later, as a half-time substitute for Bright Osayi-Samuel in a 1–0 win over local rivals Fleetwood Town at Bloomfield Road. In January 2016, having picked up an injury, Lee refused the offer of an extension to his loan and returned to West Ham. His refusal angered Blackpool manager, Neil McDonald, who was quoted as saying that Lee "would rather be at home with his mum and dad" than playing for Blackpool.
Second loan to Colchester United
On 18 January 2016, Lee signed on loan for Colchester United until the end of the 2015–16 season. He scored his first goal of his second spell on 12 March in a 3–3 draw with Wigan Athletic. He scored once more, making 15 appearances in total.
Barnsley
On 24 June 2016, Lee signed for Championship club Barnsley for an undisclosed fee. He made six appearances during the 2016–17 season, all as a substitute, but left the club by mutual consent on 4 July 2017.
Luton Town
Following his release from Barnsley on 4 July 2017, Lee signed for his former loan club Luton Town on a two-year contract. He scored in an 8–2 win over Yeovil Town on the opening day of the 2017–18 season on 5 August 2017. His contract was extended by a further year at the end of the 2017–18 season after a promotion clause was triggered as a result of Luton's promotion to League One.
