Gonçalves was born on 5 February 1979 in Gemeses, a civil parish in the city of Esposende in the Braga District of Portugal. Before transitioning to rally raid, he built an extensive competitive record across disciplines, accumulating 23 titles in motocross, supercross and enduro. His early national titles included Portuguese enduro championships in 2004 and 2005, motocross titles in 2006 and 2008, supercross titles in 2007 and 2008, and a trials national championship in 2010.
Gonçalves made his Dakar Rally debut in 2006, and went on to contest thirteen editions of the race across African, South American and Asian continents. He rode for Honda from 2006 to 2009, then moved to the BMW-owned Husqvarna team from 2010 to 2012. He also raced for KTM at various points. He returned to Honda from 2013 to 2019, before joining Hero MotoCorp for the 2020 season.
His first strong Dakar result came in 2009, when he finished tenth overall and second in the 450 cc class. By 2012 he had risen to fourth in the FIM Cross-Country Rallies World Championship. The career peak came in 2013: he finished tenth overall at the Dakar, then clinched the FIM World Championship title by winning at the Rally dos Sertoes in Brazil and the Rally OiLibya Maroc in Morocco — the latter by only a few seconds. He was runner-up in the world championship in 2014, opening that season with victory at the Abu Dhabi Desert Challenge.
The 2015 season brought his finest Dakar result: a second-place finish in the overall standings at Buenos Aires, including one stage win, with Marc Coma the only rider ahead of him. Across his thirteen Dakar starts he won three stages in total.
At the 2020 Dakar Rally, held in Saudi Arabia for the first time, Gonçalves was competing for Hero MotoCorp. During the third stage an engine problem led to a brief, erroneous announcement of his withdrawal; this was corrected after it became clear he was attempting to repair his motorcycle while waiting for team assistance.
He crashed during Stage 7 of the rally at the 276 km mark. He was found unconscious, resuscitated at the scene, and flown by helicopter to a hospital in Layla, where he was pronounced dead on 12 January 2020. He was 40 years old, less than a month away from his 41st birthday.
Following his death, the municipality of Esposende issued a statement recognising his career and describing him as an ambassador for Esposende to the world. The President of Portugal, Marcelo Rebelo de Sousa, stated that Gonçalves "died trying to achieve the dream of winning one of the hardest and most dangerous rally events in the world, in which he was always a worthy representative of Portugal, reaching second place in 2015."