For the 2014 season Henao was joined at Team Sky by his cousin Sebastián Henao.
In March 2014 Team Sky announced that they would remove Henao from the team's race schedule for eight weeks after they raised questions about the results of out-of-competition tests Henao undertook after he returned to Rionegro in October 2013 for the winter. Team Sky principal Dave Brailsford noted that the team's ability to interpret Henao's results was hampered by a lack of research into the physiology of "altitude natives" who grew up in high-altitude environments and that the team would commission independent research to shed light on the situation. Subsequently, in June 2014 the team announced that the research programme, conducted by researchers at the University of Sheffield with the cooperation of Colombian anti-doping agency, had been completed, the findings had been sent to WADA, the UCI and the Colombian Anti-Doping Federation, and that Henao would return to competition at the 2014 Tour de Suisse. However, whilst reconnoitering the time trial course with teammates, Henao was hit by a car, suffering a fractured knee cap and ruling him out for the rest of the 2014 season.
On 20 April, it was announced that Henao had been withdrawn from racing after the UCI opened a biological passport investigation against him, relating to the same readings as had caused his withdrawal in 2014. Henao himself said that he was "calm and confident that this [would] be resolved soon", while Dave Brailsford stated that "We believe in Sergio." He noted that the UCI's investigation so far had been anonymous and hoped that the UCI investigation would reach the same conclusions as the team had from the 2014 research. He was named in the start list for the Tour de France. Henao was one of Chris Froome's key mountain domestiques as he won the race for the third time.