The Australian former rider has suffered from cancer in recent years, which he says has left him unable to "do the job like I want".
Peiper was first diagnosed with prostate cancer in 2015, and in 2019 cancer was detected in a lung and rib, with extensive chemotherapy required on each occasion.
Having previously worked for BMC Racing, he joined UAE Team Emirates as a sports director ahead of the 2019 season but had to step away that spring for the rest of the season due to his health issues.
He was set to move into an advisory role at the team for 2022, but it was announced on Monday that he will be stepping back altogether.
"The treatment for cancer which I have undergone in the last six years have taken a huge toll on me mentally and physically. So much so that I don’t feel at this time that I can do the job like I want," Peiper said in a team statement.
"The last three years with UAE Team Emirates have been a wonderful experience. The team took me in knowing I had been sick and yet offered me every opportunity, immense support and understanding for which I am utterly grateful."
Peiper, who rode for the Peugot and Panasonic teams in the 1980s, began his career as a director with Lotto Soudal in 2005, going on to hold similar roles at T-Mobile/High Road, Garmin-Sharp, and BMC Racing.
He joined UAE Team Emirates ahead of the 2019 season but soon learned the cancer had returned and was forced in April to step back for the rest of the year. He returned in 2020 to guide Tadej Pogačar to his and the team's first Tour de France victory, going on to repeat the feat in 2021.
Having had to end his first stint straight after Paris-Roubaix, it was the Hell of the North - albeit a late-season edition - that was once again Peiper's last race in 2021, although the team have left the door open for a return if he feels well enough.
"Though he is stepping back, Allan will always be a member of our team. In these three years we have all learned a lot from him. His professionalism, commitment and knowledge have been invaluable to the team and we are all very grateful and thankful for what he has done," said team boss Mauro Gianetti.
"We wish him the very best and are all supporting him in his latest fight, that we know he will tackle with the same drive and determination as he always does. Allan’s place in the team will remain for good, and the door is open to him as soon as his health improves."
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