The Frenchman, who won Il Lombardia at the end of last year, hadn't raced since ending his early season block with 11th overall at the Volta a Catalunya at the end of March. However, he confirmed the quality of the training he'd done in the interim with a stage win on the Grand Colombier on the final day that handed him the overall victory.
After an opening stage for the sprinters, Pinot finished second on the Col de la Faucille on stage 2 but was left with a bitter taste as former teammate Alexandre Geniez (AG2R La Mondiale) refused to do any turns and survived his attacks before beating him to the line.
On the altogether more difficult Grand Colombier on the third and final day, Pinot chose to strike out early, reaching the top some 52 seconds ahead of Elie Gesbert (Arkea-Samsic).
"On the Grand Colombier I wanted to go on my own from early in order to climb at my own rhythm and manage my effort," Pinot said. "It's the second time I've won here, on this col that intimidates all riders."
Pinot walked off with the overall title, in which he finished 1:08 clear of Mathias Frank (AG2R La Mondiale) and 1:25 clear of Rein Taaramae (Total Direct Energie) in third.
After a two-year absence, Pinot returns to the Tour de France this year, with the Critérium du Dauphiné in June his next outing. The 28-year-old had a decent start to the season, winning the Tour du Haut Var and finishing fifth at Tirreno-Adriatico, and victory in the Ain confirmed he's on the right track for July.
"It's a nice victory. I came here to win and the mission is accomplished. I'm satisfied, with a view to what's to come – notably the Critérium du Dauphiné in two weeks," he said.
"I’ve been training well, feeling calm and well prepared after a camp in the Alps, and it was important to convert my work into a victory."