Starting from 2 February 2012, former Singaporean international footballer Fandi Ahmad began his three-year contract with Johor FA serving as the technical advisor. Later in the year, Fandi assumed the role as the team's head coach. The team eventually finished fourth in the 2012 Malaysia Premier League season.
Tunku Ismail was officially appointed as the new President of Johor FA (PBNJ) in the association's congress held on 16 February 2012. During the congress, he first mooted a proposal to revamp the whole organisation structure and its footballing activities. Part of the plan was to consolidate its football teams into a single representative competing in the Malaysian League.
During the season, there were several match fixing allegations and investigations involving players from Johor-based teams. At the end of the 2012 season, Johorean football was in a poor state. Johor based teams were underperforming and struggling in the Malaysian League. Johor FC barely avoided relegation in the Malaysian Super League, while other Johor-based clubs – Johor FA, Johor Bahru City F.C., and MP Muar F.C. – were struggling to compete in Malaysian Premier League. Just months after Tunku Ismail Sultan Ibrahim took charge as Johor FA's president, a bold strategic revamp within Johor FA (PBNJ) was initiated. The move was to realign and consolidate football teams and clubs representing Johor. It saw both teams, Johor FC and Johor FA being placed under a single management to ensure the stability of both teams. All Johor-based clubs except for Johor FC and Johor FA were withdrawn from the Malaysian League. Both teams were reinstated with same name and were placed in numerical order. In December 2012, the FAM announced that they had received the application of the team's name change to Darul Ta'zim FC for the upcoming 2013 season and with no objections to it.The team was later renamed as Johor Darul Ta'zim Football Club.
Officially, 2013 was the first year in which the Southern Tigers made its debut under the new transformation initiative. A fully refurnished Larkin Stadium was made to accommodate more fans. With the introduction of season passes, it allowed fans entry to all competitive matches for an entire season. At the start of the 2013 season, Fandi Ahmad was handed the role of head coach of the team in the Malaysia Super League, while the Malaysia Premier League team was handled by former international and Johor player, Azmi Mohamed, with the assistance of compatriot Ismail Ibrahim.Before the start of the season, Johor signed former Spanish international Dani Güiza and Italian midfielder Simone Del Nero. However, both left in the middle of the season. JDT managed to reach the 2013 Malaysia FA Cup final on away goals rule, defeating Pahang FA.In the final, JDT lost 1–0 to Kelantan FA. During the middle of the 2013 season, Fandi Ahmad was relieved of his coaching duties, but would stay on as the team's manager. Azmi Mohamed became JDT's coach on an interim basis while waiting for the arrival of a new head coach. In the first season after the club's transformation, JDT managed to finish third in the 2013 Malaysian Super League. Later on, just a day before the 2013 Malaysia Cup kicked off, Fandi Ahmad resigned as team manager and parted ways with Johor FA amicably.With the motivation to rejuvenate the glory days of the past into the future, JDT appointed former Valencia and Atlético Madrid manager Cesar Ferrando Jimenez as the new club's head coach.
In February 2014, Bojan Hodak was appointed as team manager to assist Cesar Jimenez in managerial duties.On 26 June 2014, JDT secured their first national league title by defeating Sarawak FA 1–0.In the 2014 Malaysia Cup campaign, JDT made it through to the final for the first time in 23 years, emulating the former Johor FA that won the double (league and Malaysia Cup triumphs). Billed as the "Match of Heavyweights", it was a highly anticipated match between JDT (league champions) and Pahang (Malaysia FA Cup winners). JDT lost 5–3 in the penalty shoot-out.
On 31 January 2015, JDT competed in the Piala Sumbangsih for the first time in the club's history, qualifying to the competition as the 2014 Malaysian champions. They defeated Pahang 2–0 to win the trophy.The club made their debut in the AFC Cup on 24 February 2015 with a 4–1 win over East Bengal FC in the first game of the group stage. In late April 2015, the head coach Bojan Hodak left the club and was replaced by Roberto Carlos Mario Gómez.As the new head coach, he was also given the authority to revamp youth development programmes in JDT, especially its development squads, from JDT II to JDT V.
On 12 July 2015, an announcement was made that Tunku Ismail Ibni Sultan Ibrahim left his post as president of the Johor FA; instead, he would still serve in his capacity as the Royal Patron of Johor FA. Dato' Haji Ismail bin Karim, State Secretary of Johor, was appointed as his replacement with immediate effect.In August 2015, JDT defended the Malaysia Super League title, becoming the national champions for the second year in a row. On 31 October 2015, JDT became the first Malaysian team to reach the final of the AFC Cup. In the final, held in Dushanbe, Tajikistan, they defeated the home side FC Istiklol 1–0 with a goal scored by Leandro Velazquez. As a result, JDT became the first Southeast Asian club to win a continental title.
In the opener of the 2016 season, JDT edged Selangor in a 7–6 penalty shoot-out win, successfully defending the Piala Sumbangsih title. In the same season, JDT clinched their first-ever Malaysia FA Cup title after staging a comeback 2–1 win over PKNS FC. It was the first time a club side lifted the trophy since its inception in 1990.JDT secured their third consecutive league title on Match Day 20 of the 2016 season with a 3–0 win over Terengganu.The club became the first team to win three consecutive league titles – a feat never achieved before by any team since the inception of the national league championship in 1982. Also in the 2016 season, JDT managed to end the league undefeated, thus becoming the first ever club in Malaysia to have done so.
On 18 January 2017, JDT announced that they had parted their ways with Mario Gómez barely two days before the season opener.The club promoted Mexican Benjamín Mora from JDT II to coach the squad for the 2017 season. On 21 January 2017, despite leading 1–0 at half-time, JDT were denied a third Piala Sumbangsih in a row after losing 5–4 in the penalty shoot-out to Kedah.In the 2017 AFC Champions League qualifying play-off, JDT reached the play-off round for the first time in their history, after eliminating Bangkok United in the second preliminary round after penalties. In the play-off round, JDT lost 3–0 to the Japanese side Gamba Osaka. Following on from that, Perak defeated JDT 2–1 and ended the club's record unbeaten streak of 26 league matches dating back to the opening fixture of the 2016 season.
During the 2017 mid-season break, JDT demoted Mora back into his previous position as the second team's head coach.The club appointed Portuguese Ulisses Morais as the new manager of the main squad.Morais led the team to its fourth consecutive league title; with JDT confirmed to have clinched the 2017 Super League title on 5 August 2017 with three games remaining.
During JDT Congress held in early October 2017, Tunku Ismail made several major moves in the state of Johor. All race-based football associations in the state were disbanded. However these teams will be allowed to continue participating as football clubs in the state competitions. As for the club, major restructuring of the organisation were made to ensure future success in both off and on-the-pitch. Amongst them were the appointment of Martín Hugo Prest as the new Sporting Director, meanwhile the previous Sporting Director, Alistair Edwards was reassigned as the club's Technical Director, responsible for all developmental teams including JDT II, with the team playing in the Malaysia Premier League as a developmental team instead of a feeder club.
After completing the league fixtures in late October 2017, JDT contested in the Malaysia Cup final against Kedah, the 2017 Malaysia FA Cup winners, whom they met earlier in the season opener in January. Playing in front of 80,000 fans at the Shah Alam Stadium, JDT seized the title from the "Red Eagles" with a 2–0 victory and clinched a double in the 2017 season.
In 2018, JDT were eliminated in the quarter-finals of the 2018 Malaysia FA Cup after losing to Pahang 3–0 on aggregate.JDT also failed to defend their Malaysia Cup title, losing to Terengganu in the semi-finals. During the same season, Johor won their fifth consecutive league title.