On 30 January 2010, Puncheon joined Southampton which then led to his loan deal at MK Dons to be cut short.

However, when Alan Pardew lost his job just days after a 4–0 win away to Bristol Rovers, Southampton hired Nigel Adkins as manager.

Eventually Adkins lost patience with Puncheon's erratic performances, and dropped him to the bench in favour of 17-year-old Chamberlain, who was later sold to Arsenal for a reported £15m.

[13][14] He returned to the Saints after his unsuccessful loan spell at QPR,[15] but on 21 January 2012, he publicly criticised executive chairman Nicola Cortese.

He scored his third Premier League goal in the 61st minute against Reading to secure Southampton a vital 1–0 victory and move them out of the relegation zone.

[25] On 16 August 2014, in Palace's first match of the new season away to Arsenal, Puncheon took a corner which was headed in by Brede Hangeland for the first goal of the game.

Palace manager Alan Pardew praised Puncheon's performance, describing him as "the best player on the pitch by a country mile".

[28] He opened the scoring in the 2016 FA Cup Final against Manchester United with a goal in the 78th minute, but Palace went on to lose the match 2–1 after extra time.

[31] In May 2019, Crystal Palace issued a statement that Puncheon would leave the club at the end of the 2018–19 season after having made 169 appearances and scored 16 goals.

After a year in management, Puncheon returned to playing in the 2024–25 season in Cypriot regional football with Kissos Kissonergas.

[39] On 20 November 2024, the day after leaving Ayia Napa, Puncheon was appointed head coach of Akritas Chlorakas.

[41] In December 2017, Puncheon was arrested and charged with possession of an offensive weapon, common assault, and a public order offence of "causing fear or provocation of violence" after a fight outside a nightclub in Reigate.

[44] He later changed his plea to guilty and was given a community order requiring him to carry out 210 hours of unpaid work, and pay the doorman involved £250 compensation.