Farrar is very popular in Flanders because he is fluent in Dutch and lives in the Belgian city of Ghent. In 2012, was made an honorary citizen of Ghent.
Farrar crashed four times in the 2012 Tour de France, including a sprint-finish crash, after which he stormed the Argos–Shimano team bus to confront Tom Veelers, whom he blamed for the incident. He later took his first two wins of the season at the 2012 USA Pro Cycling Challenge. In the opening stage of that race, Farrar arrived in Telluride with a field of 57 riders and won a reduced bunch sprint at the finish. Afterwards, he stated that he was surprised to have survived the mountainous terrain to be able to contend for the sprint. Farrar won again in the fifth stage of the race, dedicating the win to his former Madison partner Mike Creed, who had been raising money for the victims of the Waldo Canyon fires. Due to his two wins he consolidated enough points to win the green jersey. Later in the season, Farrar crashed heavily during the first stage of the Tour of Britain, reportedly suffering a concussion. In October, Farrar was given clearance to train by the team doctor, Prentice Steffen, who stated: "The health of the athlete is always our top priority."