Shane Sutton maintained it was in the best interests of British Cycling for him to resign as technical director - with just 100 days to go to the Rio Olympics.
The 58-year-old Australian quit after another day of allegations over his conduct.
"I believe it is in the best interests of British Cycling for me to step down from my position as technical director," Sutton said in a statement.
Sutton was suspended by British Cycling on Tuesday after it was claimed he called Paralympic cyclists "gimps", shortly after announcing an independent review into claims of sexism made by Jess Varnish.
The 25-year-old alleges Sutton told her to "go and have a baby" when dropping her from the Olympic team.
Sutton denies the allegations and said he welcomed the opportunity to address them in the review. He declined to address further claims of using racist language towards a Malaysian cyclist.
Sutton said in the statement: "It is absolutely crucial that, as our athletes begin their final preparations for Rio, they are able to do so free of distraction.
"The developments over the past few days have clearly become a distraction."
British Cycling chief executive Ian Drake said: "I understand and respect Shane's decision to stand down.
"His primary focus has always been the athletes, and this decision is something he has taken to allow them to focus on their preparation for Rio."
Programmes director Andy Harrison has taken over with immediate effect, Drake added.
Sutton continues to refute the allegations and will take part in the independent review.
Sutton succeeded Sir Dave Brailsford as British Cycling chief in 2014.
Sutton, as head coach, was then-performance director Brailsford's key lieutenant in the British team which won eight gold medals at the 2008 and 2012 Olympics. Britain won seven out of 10 track events at each Games.
Sutton is a blunt character, but there are many riders who will have had only positive experiences of his coaching and who enjoyed good working relationships with him.
Sutton rebuked his charges after the 2015 Track World Championships near Paris, but optimism returned last month when Britain topped the medal table at the 2016 event in London.
His departure could have implications for squad morale and selection, with Mark Cavendish's participation in Rio no longer as certain as it seemed.