Jones made wholesale changes to Luton's squad ahead of 2016–17, releasing 12 players and signing eight new ones. Jones' Luton team spent only one week of the season outside the top seven positions, while he also led the club to the semi-final of the EFL Trophy. He signed a new three-and-a-half-year contract with the club on 20 March 2017. Luton finished the 2016–17 season in fourth place, but were beaten 6–5 on aggregate by Blackpool in the play-off semi-final, meaning they would compete the 2017–18 season in League Two again. Jones stated his ambition to go one step further and win promotion to League One in 2017–18, saying: "This year we can't have excuses, can't have that naivety about us, can't allow teams to nick draws and cost us our ultimate goal." His summer recruitment was focused on signing experienced players who had previously won promotion, and he succeeded in doing this when signing Alan McCormack, James Collins and Marek Štěch. Luton began the season with an 8–2 home win over Yeovil Town to set a club record for their biggest margin of victory on the opening day of a season. Jones was named the League Two Manager of the Month for October 2017 after Luton recorded three wins, one draw and one defeat, including a 7–1 home victory over Stevenage. He would go on to win the award for the second successive month, in which Luton achieved three wins in four league matches, including a 7–0 home win over Cambridge United, scoring 14 goals to climb to the top of the table on goal difference. Luton's win over Cambridge meant they became the first team in the history of the English Football League to score seven or more goals on three occasions before Christmas. They were also the highest-scoring team in the country in early December with 63 goals in all competitions, one more than Manchester City who were top of the Premier League. Jones was nominated for League Two Manager of the Month for the third month in succession, which was awarded to Danny Cowley of Lincoln City. Luton topped the table until a 2–1 home defeat to Accrington Stanley in March 2018 saw them drop to second place for the first time since 21 November 2017, behind Accrington. The club did, however, win promotion to League One on 21 April 2018 after a 10-year absence following a 1–1 draw away to Carlisle United. A week later, they secured a second-place finish in the table with a 3–1 home victory over Forest Green Rovers.