[4] Sporting Goa progressed through to the final of the Federation Cup that season and met Mohun Bagan on 30 December 2006.

Khabra scored Sporting's only goal, but they lost the match in a penalty shoot-out when it ended in a tie after 90 minutes.

In the penalty shoot-out, Khabra missed his chance, but East Begal won 0–3, when Sanju Pradhan found the net in the last take of the match.

[13] He played his debut continental match as a substitute for Nirmal Chettri on 10 March 2010 against Al-Ittihad Club, which ended in a 1–4 loss for East Bengal.

[18] Khabra scored his debut goal for the club on 10 November 2012 against Air India FC, which East Bengal won 0–3 thanks to his brace.

[19][20] In the Kolkata Derby against Mohun Bagan on 9 December, in front of a crowd of 100,000, Khabra scored the opening goal of the match.

[23][24] Khabra won his last silverware of the season, when East Bengal defeated Dempo SC in the final of 2012 Federation Cup on 30 September 2012 by a score of 3–2.

[38] After the AFC Cup, he was back on pitch with East Bengal for the 2013–14 I-League season in the match against Bengaluru FC on 26 October in a 2–0 victory.

[53][54] On 22 July 2014, during the draft of the inaugural season of the Indian Super League, it was announced that Khabra was signed on loan by Team Bengaluru, which would be renamed Chennaiyin FC from East Bengal.

[58] He played an integral part in the club's progress, as they qualified for the season playoffs, meeting Kerala Blasters in both legs.

[70] He was suspended for four matches and was fined 3 lakh rupees for violating article 50 of the All India Football Federation (AIFF) disciplinary code.

[79][80] Khabra made his first appearance in the match against FC Goa on 13 October 2016 in a 2–0 victory as a substitute for Raphael Augusto.

[90] He made his first continental appearance for them in the 2017 AFC Champions League preliminary round 2 match against Al-Wehdat SC on 31 January in a 2–1 defeat.

[91] Khabra played first at the 2017 AFC Cup against Maziya S&RC on 4 April 2017 as a substitute for Sandesh Jhingan,[92] which ended in a 0–1 win for Bengaluru.

[96][97] He played his first game of the season in a 2–0 victory over Mumbai City FC on 19 November 2017,[98] in Bengaluru's first match in the Indian Super League.

[106] Khabra was benched for the match, but the club's victory helped him win his first trophy, and Bengaluru became the first ever champion of the Indian Super Cup.

[113] Khabra started in the lineup for the final against Goa on 17 March 2019,[114] which they ended up winning 1–0 after 120 minutes when a late goal decided the match for Bengaluru.

[118][119] Bengaluru qualified for the 2019–20 ISL season playoffs but failed to make it to the finals after they were brought down by ATK (former Atlético de Kolkata) with an aggregate score of 3–2.

[121] In between the ISL season, he played in the 2020 AFC Cup qualifying play-offs by appearing for the club first in the second preliminary round match against Paro FC in the first leg on 5 February 2020,[122] which they won 0–1.

[123] Khabra was back with the team for the 2020–21 Indian Super League season, which was played behind closed doors because of the COVID-19 pandemic.

[138] He suffered a muscle tweak in the training session prior to the match against his former club East Bengal on 12 December, and was omitted from the squad for the game.

[145][146] Khabra was handed a two-match ban and a fine of ₹1.5 lakh by the All India Football Federation Disciplinary Committee, after he was charged with 'violent conduct' in the Indian Super League match against Hyderabad FC in February.

[149] Khabra provided the assist from the half-way line to set up the first goal of the match scored by Adrián Luna.

[152] After the ISL campaign with Blasters, Khabra was missed out on a place in their squad to take part in the 2023 Indian Super Cup season.

[154] After his tenure with the Kerala Blasters, on 21 June 2023, Khabra was re-signed by East Bengal as a free agent after seven years since his departure in 2016 ahead of the 2023–24 season.

[155] He made his return at 2023 Durand Cup captaining the side in a 2-2 draw against Bangladesh Army Football Team, providing an assist to Javier Siverio's goal.

On 24 September 2022, Khabra made his first appearance for India since 2016 by coming as a substitute for Naorem Roshan Singh in the 68th minute in a 1–1 draw against Singapore.