On 29 May 2008, McCombe agreed a two-year contract to join Port Vale.
He claimed one of the reasons he put pen to paper was that having met manager Lee Sinnott 13 years previously, he knew that Sinnott could help improve his game.
However, he established himself as a first-choice centre back under new manager Dean Glover, but was also told he was too 'nice' and needed to be more aggressive in his defending.
Nevertheless, his performances 2008–09 earned him the chairman's Player of the Year award, as well as the nickname 'Boom Boom McCombe' from fans.

Retaining his first-team place in 2009–10, he was transfer listed in late September 2009, along with the entire Port Vale squad, after manager Micky Adams saw his team slip to a third consecutive defeat.
However, by the end of October 2009 he had played in the opening 18 matches of the season, picking up a goal on the way, and was confident of earning a new contract by the season's end.
On 12 December 2009, he received the first sending off of his career, following a professional foul on Northampton Town's Adebayo Akinfenwa.
This brought to an end his run of 29 consecutive starts, and kept him out of the team for the next six weeks, as manager Micky Adams switched his tactics during McCombe's absence, moving from a 3–5–2 to 4–4–2 formation.
He was offered a new two-year contract by the club at the end of the season, which he quickly signed.

He started 2010–11 in fine form, and his strong performances in November 2010 saw him nominated for the League Two player of the month award.
His strong performances continued throughout the season, and he was rewarded with the club's Player of the Year award.

Adams continued to use McCombe in the heart of the Vale defence at the start of 2011–12, however he dropped him from the first team after 11 matches in favour of loan signing Liam Chilvers.
He marked his return to the first team on 14 October 2011 with the second goal of a 3–0 win over Northampton Town.
However, he was dropped after the next match, a 4–0 defeat at home to Morecambe, only to win back his first-team place the following month after turning down the chance to leave the club on loan.
With the loanees back at their parent clubs, Gareth Owen out injured and Clayton McDonald in court, McCombe helped to guide teenage centre back Joe Davis through the final stages of the season.
He agreed to sign a new two-year deal with the club in June 2012.

He formed a solid centre-back partnership with Clayton McDonald at the start of 2012–13.
 On 25 August, he scored in a 3–1 win over Morecambe at the Globe Arena, earning himself a place on the League Two team of the week.
On 27 October, he was sent off for the second time in his career, again against Northampton at Sixfields, as he put in a late challenge on midfielder Alex Nicholls, who managed to score the opening goal of the match just before McCombe made his challenge; it was later confirmed that the tackle had broken Nicholls's leg.
Opposition manager Aidy Boothroyd accepted McCombe's apology, and Northampton player Akinfenwa also stated that McCombe was "not a malicious character".
McCombe himself picked up an injury on 1 January 2013, damaging knee ligaments in a defeat to Fleetwood Town, and was ruled out of action for several weeks.
Vale secured promotion with a third-place finish at the end of the season, with McCombe playing 37 matches in a regularly changing four back.
Despite still being under contract, he chose to leave the club in the summer.
On 29 May 2008, McCombe agreed a two-year contract to join Port Vale. He claimed one of the reasons he put pen to paper was that having met manager Lee Sinnott 13 years previously, he knew that Sinnott could help improve his game. However, he established himself as a first-choice centre back under new manager Dean Glover, but was also told he was too 'nice' and needed to be more aggressive in his defending. Nevertheless, his performances 2008–09 earned him the chairman's Player of the Year award, as well as the nickname 'Boom Boom McCombe' from fans.
Retaining his first-team place in 2009–10, he was transfer listed in late September 2009, along with the entire Port Vale squad, after manager Micky Adams saw his team slip to a third consecutive defeat. However, by the end of October 2009 he had played in the opening 18 matches of the season, picking up a goal on the way, and was confident of earning a new contract by the season's end. On 12 December 2009, he received the first sending off of his career, following a professional foul on Northampton Town's Adebayo Akinfenwa. This brought to an end his run of 29 consecutive starts, and kept him out of the team for the next six weeks, as manager Micky Adams switched his tactics during McCombe's absence, moving from a 3–5–2 to 4–4–2 formation. He was offered a new two-year contract by the club at the end of the season, which he quickly signed.
He started 2010–11 in fine form, and his strong performances in November 2010 saw him nominated for the League Two player of the month award. His strong performances continued throughout the season, and he was rewarded with the club's Player of the Year award.
Adams continued to use McCombe in the heart of the Vale defence at the start of 2011–12, however he dropped him from the first team after 11 matches in favour of loan signing Liam Chilvers. He marked his return to the first team on 14 October 2011 with the second goal of a 3–0 win over Northampton Town. However, he was dropped after the next match, a 4–0 defeat at home to Morecambe, only to win back his first-team place the following month after turning down the chance to leave the club on loan. With the loanees back at their parent clubs, Gareth Owen out injured and Clayton McDonald in court, McCombe helped to guide teenage centre back Joe Davis through the final stages of the season. He agreed to sign a new two-year deal with the club in June 2012.
He formed a solid centre-back partnership with Clayton McDonald at the start of 2012–13.  On 25 August, he scored in a 3–1 win over Morecambe at the Globe Arena, earning himself a place on the League Two team of the week. On 27 October, he was sent off for the second time in his career, again against Northampton at Sixfields, as he put in a late challenge on midfielder Alex Nicholls, who managed to score the opening goal of the match just before McCombe made his challenge; it was later confirmed that the tackle had broken Nicholls's leg. Opposition manager Aidy Boothroyd accepted McCombe's apology, and Northampton player Akinfenwa also stated that McCombe was "not a malicious character". McCombe himself picked up an injury on 1 January 2013, damaging knee ligaments in a defeat to Fleetwood Town, and was ruled out of action for several weeks. Vale secured promotion with a third-place finish at the end of the season, with McCombe playing 37 matches in a regularly changing four back. Despite still being under contract, he chose to leave the club in the summer.
John McCombe