However, Hartlepool secured an immediate return to League One as runners-up with Nelson earning a place in the PFA Team of the Year for his performances.

[10] On 27 April 2001, Nelson quickly made an impact on his Bury debut when he "struck a sweet half volley into the top corner", in a 1–1 draw against Wycombe Wanderers.

[15] Teammate Steve Redmond praised his performance, describing him as "an old fashioned centre half and he'll keep learning all the time and hopefully he'll progress throughout the season.

At the start of the 2002–03 season, Nelson was initially dropped from Bury's first-team squad, but he quickly regained his first team place, forming a defensive partnership with Danny Swailes.

[7][38] Upon joining the club, manager Cooper said he expected Nelson to "be a major star for Hartlepool United" next season, describing him as "a very commanding and is a big strong lad" and "can get up and down the pitch and is dominating in the air".

Nelson began to form a strong partnership with Chris Westwood and the pair played together for the majority of the club's matches.

[48] After regaining his fitness due to a knock, he played in both legs of the club's play-off semi-final match against Bristol City, as Hartlepool lost 3–2 on aggregate.

[60] In the League One play-off final against Sheffield Wednesday, Nelson started the match, as Hartlepool United loss 4–2 in front of a crowd of 59,808 at the Millennium Stadium.

[63] On 15 October, however, Nelson received his first red card for Hartlepool after he retaliated and elbowed Jack Lester during the club's 2–0 defeat against Nottingham Forest.

[72] On 26 December 2006, Nelson suffered medial ligament injuries in his left knee and was substituted in the 33rd minute, in a 2–0 win against Grimsby Town.

[79] On 9 April 2007, he started the whole game and helped the club keep a clean sheet, in a 1–0 win against Accrington Stanley, resulting in Hartlepool United earning promotion back to League One.

[83] Nelson was also named in the PFA League Two Team of the Year for the 2006–07 season, alongside teammates Ritchie Humphreys and Andy Monkhouse.

[91] With his contract expiring at the end of the 2008–09 season, Nelson was linked with a move to Leicester City in the January transfer window, but manager Danny Wilson dismissed suggestions of the player leaving Hartlepool United.

[92] On 3 January 2009, he scored his second goal of the season, in a 2–0 win against Premier League side Stoke City in the third round of the FA Cup.

[93] On 24 January 2009, Nelson was penalised for handball, resulting in a penalty, in a 2–0 loss against Premier League West Ham United in the fourth round of the FA Cup.

[97] Despite having seven stitches in a head wound sustained during Hartlepool's loss against Leeds United, Nelson passed fit and started the match against Bristol Rovers on the last game of the season, as the club lost 4–1 but nevertheless avoided relegation.

[100] By June, the chances of the player staying was "receding", with clubs, such as, Hibernian, Scunthorpe United and Norwich CIty were interested in signing him.

[110] He subsequently formed a strong central defensive partnership with Gary Doherty as the Canaries surged up the League One table, overhauling runaway leaders Leeds United in the process.

[111] On 17 April 2010, Nelson scored the only goal in a 1–0 victory at Charlton Athletic which secured Norwich City's return to the Championship at the first attempt.

[127] Upon joining the club, manager Kenny Shiels described new signing Nelson as 'quality' and expected the player to be a good asset in the second half of the season.

[129] On 28 January 2012, he made his debut for Kilmarnock, starting the whole game in the central defence position, in a 1–0 win against Ayr United in the semi–finals of the Scottish League Cup to help the club reach the final.

On 1 August 2013, Nelson signed a two-year deal with Scottish Premiership side Hibernian, moving from Bradford City for a nominal transfer fee.

[147] On 2 January 2014, he set up a goal for James Collins to break the deadlock after 61 minutes to the match, in a 2–1 win against local rival, Hearts.

[152] During 2–1 loss against local rivals, Hearts on 17 August 2014, Nelson received an elbow in the face by Osman Sow that saw him sent–off, but he quickly recovered.

[154] On 26 August 2014, Nelson signed a one-year contract with League Two side Cambridge United shortly after agreeing mutual termination with his previous club Hibernian.

On 1 June 2017, he signed a new deal at the end of the season and extended his contract into a third year in summer 2017, as well as, taking up a role as the club's under-23 team coach.

[189] On 10 August 2019, he made his début for the club, starting a match and played 67 minutes before being substituted, in a 0–0 draw at AFC Telford United.

[201] During the 2020–21 season, he once came out of retirement as a replacement for the suspended Matthew Elsdon and played in the FA Cup match against Marske United, as the club loss 1–0.

[202] Following Blyth Spartans' injury crisis, Nelson made his first league appearance for the club, starting the whole game, in a 3–0 loss against York City on 2 December 2020.

[216] Following Scunthorpe United's takeover and appointment of a new permanent manager in Jimmy Dean, Nelson was retained as head coach.