Johor FC were the first club team in the Malaysian football league system to enter the Malaysia Cup in 2000 under English manager Bruce Stowell.

The Malaysia Cup was previously dominated by state teams and by defeating ATM on aggregate in the second-round group qualification, the club marked another record in the competition.

[9] Starting from 2 February 2012, former Singaporean international footballer Fandi Ahmad began his three-year contract with Johor FA serving as the technical advisor.

[15][16] 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.

[15] Before the start of the season, Johor signed former Spanish international Dani Güiza and Italian midfielder Simone Del Nero.

[25][26] 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.

[27] 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.

[38][39] In late April 2015, the head coach Bojan Hodak left the club and was replaced by Roberto Carlos Mario Gómez.

In the final, held in Dushanbe, Tajikistan, they defeated the home side FC Istiklol 1–0 with a goal scored by Leandro Velázquez.

[44][45][46] In the opener of the 2016 season, JDT edged Selangor in a 7–6 penalty shoot-out win, successfully defending the Piala Sumbangsih title.

[47] In the same season, JDT clinched their first-ever Malaysia FA Cup title after staging a comeback 2–1 win over PKNS FC.

[60][61] 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.

[67] During JDT Congress held in early October 2017, Tunku Ismail made several major moves in the state of Johor.

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.

[75] On the eve of the 2016 season, JDT officially came under the ownership of Tunku Ismail in a statement released by Johor FA dated 10 January 2016.

It further clarified that JDT were now turned into a full-fledged professional outfit, as a separate entity from the Johor FA which organises the overall football development programme in the state.

[76] A day later, former Johor striker who was a key member of the historic double-winning team of 1991, Alistair Edwards was appointed as JDT's Sporting Director to assist Tunku Ismail.

[77] The move was seen as part of the privatisation process and a strategic initiative on how Malaysia football clubs should be run and managed professionally including the youth development in the region.

[86] The foundation's Membership Card launch was held at the Persada International Convention Centre in Johor Bahru on 7 December 2016.

The new kits were officially unveiled with a commercial video featuring JDT footballers inside the Senai International Airport terminal.

[102] Beginning in 2013, with JDT's resurrection and emergence as one of Malaysia's football powerhouse to fight for the league titles and other domestic cup campaigns, Felda United became one of the club's main rivals.

Between 2013 and 2016, the two sides met on 12 occasions, with JDT triumphant six times, Felda United thrice, with the remaining three games being draws.

Besides the indoor synthetic field measuring 16 x 109.2 metres, the building comes with the gym equipment, a swimming pool, and ice baths.

[118][119] After its design plans were approved on 24 December 2014, the groundbreaking ceremony of the all-weather training arena was held on 1 January 2015, attended by Tunku Aminah.

[120][121][122] The development of the RM15 million indoor facility was sponsored by Iskandar Waterfront Holdings (IWH) under its Corporate Social Responsibility (CSR) programme.

[123] After its completion, it was named the Dato Suleiman Mohd Noor Indoor Training Centre as a special recognition and appreciation for his contribution as the "Father of Johorean Football" on 23 February 2016.

[124][125] To demonstrate his ideas and commitment to youth development in the state, Tunku Ismail has entered into partnerships and built ties with various football individuals all over the world.

To date, JDT has developed strategic partnership and collaborations with Borussia Dortmund (Germany), Hokkaido Consadole Sapporo (Japan), and Valencia (Spain).

[126][127][128] Besides signing new young players for development, the club has been organising competitive tournaments across all age groups in the districts of Johor.

[129][130][131] As of December 2015, the club is in the process of building a brand new youth academy with up to 15 football pitches and modern facilities, designed in collaboration with Borussia Dortmund, who have entered into a partnership with JDT.