His first start came in the next match, a Football League Trophy first-round tie at Rotherham United on 1 September, which Town won 2–1.

[14] He made his debut at St Mirren Park on 8 January, when he started against Peterhead in a Scottish Cup tie.

[22] Goodwin scored yet another goal from distance in a home SPL tie against Hearts, driving the ball past opposing keeper Jamie MacDonald from 40 yards with a terrific strike.

[25] On 30 December 2013, Goodwin was given a two-match suspension after St Mirren accepted the offer of the ban from the SFA's compliance officer, following a clash with Stuart Armstrong of Dundee United in a match four days earlier.

[26] On 13 May 2014, Goodwin signed a new two-year contract with the club, taking on a player-coach role to assist newly appointed St Mirren manager Tommy Craig.

Goodwin was at the heart of the defence for the Republic of Ireland under-16 along with fellow Waterford man John O'Shea, as they won the 1998 UEFA European Under-16 Football Championship in Perth, Scotland.

[42] A 1–0 win against last-placed Hearts in the last league match before competitive football was stopped by the COVID-19 pandemic meant that St Mirren finished ninth in the 2019–20 Scottish Premiership.

[43][44] Goodwin signed a new contract with St Mirren in February 2021, with the team sitting in 7th place in the 2020–21 Scottish Premiership.

[45] In February 2022 Aberdeen met the terms of a release clause in Goodwin's contract allowing him to end his time at St Mirren.

[47] On 19 February 2022, Goodwin was appointed manager of Aberdeen on a two-and-a-half-year contract following the sacking of Stephen Glass.

Having won only two of Goodwin's first twelve league games as manager, Aberdeen finished the 2021–22 Premiership season in tenth place, their lowest position in eighteen years.

[51] Goodwin made substantial changes to the squad with 26 players joining or leaving Aberdeen before the start of the 2022–23 season.

[52] In October 2022 Goodwin was given an eight-match touchline ban for remarks made about Hibernian player Ryan Porteous, who had won a controversial penalty against Aberdeen the previous month.

[54] In January 2023, Goodwin came under pressure during a run of results which included a 5–0 league defeat by third-placed Hearts, followed by a 1–0 Scottish Cup loss to Darvel.

[55] The defeat by the West of Scotland Football League (sixth tier) team was described as Aberdeen's worst result in their 120-year history.

[56][57] Club chairman Dave Cormack subsequently released a statement saying: "Jim has been left in no doubt that the Board and the fans are seeking an immediate response from him and the players.”[58] Aberdeen lost their next game 6–0 away to Hibernian in the league[59] in a game termed “El Sackio” (a play on words of El Clásico) due to the precarious position of both managers;[60] this was Aberdeen's largest magnitude of defeat to Hibernian in their history.

[62] In March 2023 Goodwin was appointed manager of Dundee United on a short-term contract until the end of the 2022–23 Scottish Premiership.

At the time of Goodwin's appointment, the team were four points adrift at the bottom of the league with twelve games remaining.

[65] Three wins in a row during April lifted the team from the foot of the league table, but five consecutive defeats in May left the club in last place and relegated to the Scottish Championship.

[70] Goodwin also changed systems to a preferred 3-4-3 for the upcoming season stating “That’ll give us the best chance to win games.

In November 2024 it was announced that Goodwin had signed a contract extension with Dundee United which would see him remain manager until at least the summer of 2026.