In February 2015, despite getting some good results, the club replaced him with Jose Riga midway into the season citing lack of experience as a head coach.

[6] He was offered the assistant manager role under Riga, to which he responded; "To propose to me to remain in the staff, it is only to be politically correct towards the players and the supporters.

[10] On 17 June 2021, Kerala Blasters announced that Vukomanović has been appointed as the Indian Super League club's new head coach ahead of the 2021–22 season.

[11][12] Under Vukomanović, Kerala Blasters won their first game of the season in the 2021 Durand Cup match against Indian Navy with a score of 0–1 on 11 September 2021.

[13] His first Indian Super League match as the manager of Kerala Blasters ended in 4–2 defeat on 19 November against ATK Mohun Bagan FC.

[20][21] The Blasters' unbeaten streak under Vukomanović continued, and they moved to the top of the table for the first time in eight years during the mid-season after the 1–0 victory over Hyderabad FC on 9 January 2022.

[22] Under his management, the Blasters qualified for the ISL finals for the first time since 2016 after beating Jamshedpur FC 2–1 on aggregate score from both legs.

[24] The club reached numerous milestones during the season including a 10-match unbeaten run which made them climb to the top of the table for the first time in its history.

[28] The 2022–23 Indian Super League began on a high note with a 3–1 victory over SC East Bengal on 7 October 2022 which was also his first home game as the Blasters manager after the regular home-away format returned after the COVID-19 regulation.

[35] On 7 February, the Blasters registered their 10th win during the 2022–23 Indian Super League season after defeating Chennaiyin FC 2–1 at home.

[41] Kerala Blasters forfeited the match after claiming that the referee Crystal John did not blow the whistle before Chhetri took the kick and the players were not ready in their defensive positions.

[43] Kerala Blasters later alleged that the referee asked Luna to move away from ball and hence the free kick should have only been allowed following a whistle.

[45][46] The AIFF DC that met on 31 March then imposed a 10-match ban along with a fine of 5 lakhs Indian rupees on Vukomanović for 'the abandonment and bringing the game into disrepute' under the Article 9.1.2 of the AIFF disciplinary code and directed Vukomanović to issue a public apology within a week, failing which the fine would be doubled to 10 lakhs Indian rupees.

[48] After serving his ten-match ban, Vukomanović made his come-back to Blasters' dugout as their head-coach in the 2023–24 Indian Super League season in the home game against Odisha FC on 27 October, where he was welcomed back by the fans with a tifo.

[51] After the 1–0 away victory against Mohun Bagan SG on 27 December, Vukomanović became the first manager in Kerala Blasters' history, under whose tenure they defeated all the possible opponents in the ISL.

At the time of his departure, Vukomanovic was the only Kerala Blasters FC head coach to have a positive goal difference across his reign.

[57] Vukomanović usually lines up his team in a 4-4-2 formation with two playmakers pushed outside and two high-pressing forwards, but the lineup would change slightly depending on who played where.