For the 2013 season, Barguil joined the team as a regular rider, and booked his largest victories up to that point of his career, when he won stages 13 and 16 of the Vuelta a España.

Barguil took no other wins this season, but placed 4th in the Rund um Köln and 8th in the Grand Prix d'Ouverture La Marseillaise.

Barguil opened the Tour de France with a great first week, finishing 13th atop the Mûr-de-Bretagne and was in 8th position overall after that stage.

On 23 January 2016, Barguil was one of the six members of the Team Giant–Alpecin who were hit by a motorist who drove into oncoming traffic while they were training in Spain.

After his Stage 18 win, Barguil had an insurmountable 89-point lead over second-placed Primož Roglič at the top of the mountains classification.

After a rough beginning to 2019, Barguil won the French National Road Race Championships, in a sprint finish.

[23] When racing resumed in the summer, Barguil recorded top-ten overall finishes at the Route d'Occitanie and the Critérium du Dauphiné.

[26] Prior to the Tour de France, Barguil finished fourth in the French National Road Race Championships in Épinal.

[27] In August, Barguil finished eighth overall at the Arctic Race of Norway, before winning the Tour du Limousin on the final day,[28] after overnight leader Dorian Godon lost over two minutes.

[29] After five top-ten results in the early part of the 2022 season, Barguil recorded his first UCI World Tour victory since the 2017 Tour de France,[30] with a win on the fifth stage at Tirreno–Adriatico; he soloed clear of his breakaway companions at the start of the final climb to Fermo, ultimately holding onto a 10-second winning margin over Xandro Meurisse.

[31] His next start came at the snowy GP Miguel Induráin, where he won a small group sprint of some ten riders to take victory.

[34] He featured in the breakaway during the sixth stage of the Critérium du Dauphiné, but finished third behind Valentin Ferron and Pierre Rolland.

[35] Barguil finished fourth in the French National Road Race Championships[36] – for the second year in succession – ahead of the Tour de France, from which he ultimately withdrew due to a positive test for COVID-19.

[40] Having recorded a fourth top-ten finish in as many years at the 2023 La Flèche Wallonne with tenth place,[41] Barguil made his first start at the Giro d'Italia, as team leader for Arkéa–Samsic.