Gonalons had been with Olympique Lyonnais since the age of 10 climbing through the club's youth sections after joining the club from local outfit FC Villefranche. For the 2007–08 season, at the age of 18, he was promoted to the club's Championnat de France amateur team appearing in 26 matches scoring two goals. Lyon finished in a respectable 7th in their group, but weren't allowed progression to the playoffs. The next season, he again spent with the CFA squad, however, during the summer leading up to the season, Gonalons picked up a staph infection on his ankle, which was, at one point, deemed career threatening with reportedly future diagnosis of sepsis and amputation. However, over the course of the season, Gonalons gradually got back into playing shape and eventually returned to the team. He made 24 appearances scoring 3 goals, one each against local rivals AS Lyon Duchère and Saint-Étienne, and one against Marignane. Lyon finished first among professional clubs in the group and qualified for the playoffs. Gonalons started both the 4–3 semi-final win on penalties and the 3–0 victory over Sochaux in the final picking up a yellow card.
Lyon
Following the season, on 6 July 2009, Gonalons signed his first professional contract agreeing to a one-year deal with the club. The club does have the option to keep him for the next two seasons over after the one-year deal expires. Gonalons was assigned the number 41 shirt and trained with the senior team during pre-season. He made his professional debut on 25 August 2009 in the second leg of the club's UEFA Champions Leagueplayoff round match against Anderlecht appearing as a substitute in the 73rd minute for Jérémy Toulalan. On 20 October, after coming on as a 42nd-minute substitute for the injured Brazilian Cris, Gonalons scored his first professional goal against Liverpool at Anfield, in the 72nd minute, in the UEFA Champions League. The equalizing goal drew the match level at 1–1 and Lyon went on to win the match 2–1 with a goal from César Delgado in injury time. On 16 January 2010, Gonalons scored his first career league goal against Nancy. Ten days later, Gonalons and Lyon agreed to contract extension, which will keep the midfielder at the club until 2014. Gonalons played a total of 330 games for Lyon and is eighth on the all time appearance list for the club.
Roma
On 3 July 2017, Gonalons signed a four-year contract with Roma.
