Though born in Guinea-Bissau, Gonçalves is a naturalised citizen of Portugal. He has represented them at under-17 level. In 2010, he was called up to the Portugal under-20 team to participate in training sessions as the team was preparing for the 2011 FIFA U-20 World Cup. Gonçalves, however, showed up to the camp out of shape and was, ultimately, not considered for the tournament by coach Ilídio Vale.

Gonçalves was born in Bissau, the capital city of Guinea-Bissau, but moved to Portugal with his family at the age of three. He began his football career with Boavista. Gonçalves spent three years at the club before venturing to France to sign with Nice after being invited for a trial at the club. Prior to signing with the club, he drew interest from English club Liverpool. Gonçalves spent two years in Nice’s youth academy before earning promotion to the club’s reserve team in the Championnat de France amateur 2 for the 2010–11 season. Following a successful half season at reserve level, he was called up to the senior team in January 2011 and made his professional debut in a 2–0 defeat to Bordeaux, appearing as a substitute. That was his only senior team appearance of the campaign.

On 30 June 2011, Gonçalves signed his first professional contract, agreeing to a three-year deal until 2014. He was officially promoted to the senior team by manager Éric Roy and assigned the number 24 shirt for the 2011–12 season. He scored twice that season, including the winner in a 4–3 victory at Lyon on the last day, 20 May 2012.

On 3 August 2012, Nice confirmed on its official website that Gonçalves would be returning to Portugal to join first division club Rio Ave. Gonçalves had previously expressed his desire to join the Vila do Conde-based club in order to be near his family.

On 22 January 2013, Gonçalves signed on loan with Scottish Premier League club St Mirren until the end of the 2012–13 season. The day after signing, he was quoted in the local newspaper Paisley Daily Express that he could be “the next Drogba”.

On 17 March 2013, Gonçalves played in the Scottish League Cup final against Hearts where he scored the equalising goal and provided an assist for Conor Newton’s third in a 3–2 victory Buddies’ first League Cup and their first major trophy since 1987. Shortly after scoring, he lifted his jersey, which had the inscription “Forca Fábio Faria” (“Come on Fábio Faria”), dedicating a goal to a player whose career ended after a heart condition. Gonçalves was then booked by the referee.

On 3 July 2013, Gonçalves completed a season-long loan move to Cypriot side APOEL.

On 14 January 2014, Veria signed Gonçalves on a one-year loan deal. He scored his first Superleague goal in a defeat to PAOK.

After a stint in Cyprus with Anorthosis, Gonçalves signed for Scottish Premiership club Heart of Midlothian in January 2017. Hearts paid a transfer fee of about £170,000 for his services and he made his debut in a 4–1 win over Rangers on 1 February. Gonçalves scored 15 goals in 42 appearances for Hearts, until he was sold to Pakhtakor Tashkent for £350,000 in January 2018.

Gonçalves signed for Uzbek club Pakhtakor Tashkent in January 2018.

He earned one cap for Guinea-Bissau on 22 March 2018, starting in a 2–0 friendly loss to Burkina Faso in Limeil-Brévannes, France.

On 26 January 2019, Gonçalves moved to Esteghlal on an 18-month-long contract. He was given the squad shirt number 20. He made his debut for the club on 7 February, in a 4–0 win against Paykan, coming on as an 81st-minute substitute for Morteza Tabrizi. He scored his first goal for Esteghlal in the same game just two minutes after coming on as a substitute. On 1 June, Esteghlal announced Isma’s contract was terminated by mutual consent.

Gonçalves signed for Japanese club Matsumoto Yamaga in September 2019. On 23 November, he made his debut for the Japanese side as a substitute in a 1–0 defeat against Yokohama F. Marinos.

On 11 October 2020, Gonçalves joined Indian Super League club Chennaiyin FC on a one year contract.