Ipswich Town
Aged 21, Johnson joined Bobby Robson's Ipswich Town in autumn 1972 in exchange for Ipswich's top scorer, Rod Belfitt, plus £40,000 going to Goodison. The transfer date is disputed, reported in some sources as 30 October and in some sources as early November. Robson heavily utilised the Ipswich youth system, making Johnson one of just 14 players Robson signed in his 13 years managing Ipswich. Johnson forged a powerful strike partnership with Trevor Whymark, supported by the industrious Bryan Hamilton and the clever Colin Viljoen both weighing in with goals from midfield. Johnson's move to Ipswich was later described as "a perfect fit at Portman Road where Bobby Robson was laying the foundations of the thirteen-year reign in charge which would ultimately land him the England manager's job."
Known at Ipswich as "Jonty", he debuted for them on 4 November 1972 in a 2–2 league draw hosting Don Revie's Leeds United. Johnson assisted Whymark putting Ipswich 2–1 ahead in what was reported as Johnson having "a fine debut". Johnson's first Ipswich goal was on 2 December the same year, drawing 1–1 in the league at Manchester City with a first time left foot equaliser from inside the box. That was the first of four Johnson goals in three games (all in the league), including a double against Crystal Palace in a 2–1 home win. On 17 February, Johnson's headers from set-pieces led to two Hamilton goals, winning 4–1 in the league against Manchester United before the then-record 31,857 Portman Road crowd. Johnson played on 10 March when that Portman Road record was surpassed when 34,632 saw Arsenal win in the league 2–1. Another of his goals that season was when losing 2–1 in the league at Liverpool on 24 February.
He played in every league game that season after signing with Ipswich. They lost only six of their final 27 league games as they finished fourth, qualifying for the UEFA Cup. Ipswich won the 1972–73 Texaco Cup final 4–2 on aggregate (both 2–1 victories), over East Anglian derby rivals Norwich City. Johnson did not play in the away second leg. Johnson ended his opening Ipswich season with eight goals from his 33 games, and a call-up to the England U23s.
In the UEFA Cup first round, Ipswich won 1–0 at home and drew 0–0 in front of 80,000 fans away, eliminating Real Madrid. In the second round, visitors Lazio were 4–0 down in the first leg. Giancarlo Oddi's waist high challenge caused Johnson's stretchering off, needing scrotal stitches. Johnson consequently missed Ipswich's next three games. Johnson returned to the bench for the second leg in Rome. Pre-kickoff, Trevor Whymark was handed a commemorative trophy by a group of Roma fans for his four first leg goals against their arch-rivals. That Roma provocation sparked Lazio ultras and players to an evening of violence. Johnson subbed on in the 83rd minute. Giorgio Chinaglia soon after scored his third of the game to put the tie back in the balance, 4–1 on the night (5–4 on aggregate to Ipswich). Johnson's low left foot finish from just outside the box then settled the tie 6–4. "Believe me, it was not football, it was war." Robson said afterwards.
Ipswich beat Frans Thijssen and FC Twente home (1–0) and away (2–1) in the third round. Ipswich then lost the quarter-final to Locomotiv Leipzig 4–3 on penalties. Both legs were 1–0 home wins. Mick Mills was sent off in the 40th minute of the away second leg with the score at 0–0. 57,000 fans attended. Johnson was the second of three Ipswich penalty takers in the shootout in East Germany who failed to convert. He scored 15 times in 54 games that season. His goals included league doubles at West Ham United) in a 3–3 draw and Chelsea in a 3–2 win. He also scored again at Liverpool, this time losing 4–2 on 17 November. He scored the equaliser in the 2–1 derby win at Norwich City on 26 December. Ipswich again finished fourth in the league, qualifying for the UEFA Cup.
In the UEFA Cup first round, Frans Thijssen and FC Twente eliminated Ipswich on away goals (2–2 in Ipswich, then 1–1 in Enschede). Ipswich domestically chased the league and FA Cup double. On 2 November, hosting top of the table Liverpool, Johnson evaded Emlyn Hughes and Chris Lawler to assist Brian Talbot, winning the match 1–0. Ipswich topped the table after a 2–0 home win over Middlesbrough on 11 January, with Johnson's right foot shot from the just outside the box the second goal. All Ipswich FA Cup opponents were fellow First Division clubs. Johnson scored in the third round round 2–1 win at Wolverhampton Wanderers. He played in the fourth round, eliminating holders, Liverpool, 1–0 at home. 34,709 watched to surpass the crowd of Arsenal's 1973 visit. His goal at 0–2 down in the fifth round hosting Aston Villa, sparked a comeback 3–2 win. He also played the key pass to Talbot leading to Bryan Hamilton's equaliser.
They needed three "stamina sapping" March FA Cup quarter-final replays to eliminate Leeds United. Johnson started all four games, including the 0–0 first of the four, setting a 38,010 Portman Road crowd record that still stands. Johnson headed Ipswich ahead in the away 1–1 first replay. The third game was another 0–0, this time at neutral Filbert Street. Johnson was subbed off injured in the 37th minute of the fourth game, a 3–2 win played at Filbert Street again. He consequently missed Ipswich's next five games. Johnson thus missed the April semi-final 0–0 draw with West Ham United, and the 2–1 replay loss.
He also missed the 31 March, 0–0 league game at soon-to-be relegated Chelsea. Results elsewhere that day meant Ipswich missed the chance to top the league for the first time since mid-January. That league season Ipswich, "made the early running, but fixture congestion and a relatively thin squad got the better of them." Title contenders Ipswich (2–1 at Leeds), Liverpool and Everton all lost on the league season's penultimate Saturday on 19 April. Ipswich drawing their game in hand 1–1 four days later at Manchester City won the title that day for Dave Mackay's Derby County. Ipswich finished third in that league season, two points behind, but consoled by their third consecutive UEFA Cup qualification. Johnson again scored 15 goals in a season, this time in 48 games. That included a hat-trick, beating Coventry City 4–0 at home on 16 November. He scored another derby goal against Norwich City, losing 2–1 in the League Cup fifth round home replay on 10 December 1974.
His four goals in five games near the beginning of the season included the opener in the 2–0 league win hosting Liverpool on 13 September. Four days later, Johnson scored the winner in a 2–1 victory over Feyenoord in the first leg first round of the UEFA Cup. That was followed up by a 2–0 second leg home win. Against Club Brugge in the second round, Ipswich won 3–0 at home but went out losing 4–0 in the away tie. Johnson and Ipswich ended the league season in sixth, the lowest of his four Ipswich seasons. He scored eight goals in 43 games. One of his goals included heading home Eric Gates' cross to pull back to 3–2 in the 3–3 league draw at Everton.
Johnson scored 46 goals in 178 Ipswich appearances. In Johnson's four Ipswich seasons, they finished in the top division fourth (twice), third and sixth respectively. In 1976, Tottenham Hotspur unsuccessfully bid around £200,000 for him. Johnson later said though, "I had four great years under Bobby Robson and there was only one club that would have prised me away from Portman Road and that was Liverpool."
Johnson was later inducted into the Ipswich Town Hall of Fame in 2016.