Lewer worked as assistant to Jimmy Quinn at Cambridge United
Histon have confirmed that Alan Lewer is no longer manager of the Blue Square Premier club.
The Stutes advertised the position, stating Lewer was out of contract but welcome to re-apply for his old job.
Histon chief executive Allen Soraff said: "Alan undertook a temporary role until the end of the season but declined to apply for the role.
"We are now conducting interviews. We hope to be able to make an announcement on an appointment in the near future."
He added: "As a board of directors we thank Alan for his hard work and commitment during the latter part of last season and wish him all the very best for the future."
The former Weymouth boss initially refused to apply for the job because he believed he had a legal commitment to be Stutes boss.
He told BBC Radio Cambridgeshire: "I won't be applying for my position. Legally I know I'm still in a job here."
Lewer led the Stutes to safety in the Blue Square Premier this season after taking over from previous boss Steve Fallon.
He added: "I was told that if I kept the club in the Blue Square Premier I would have another year to go."
Lewer initially arrived at Histon in October 2009 as assistant to Fallon.
He took charge of first-team affairs after Fallon was sacked in January, but managed just three league wins in 22 matches.
"I'm not applying for a job I'm already in. They asked me if I was applying for the job and I told them I would not be," he said.
Lewer's reign has been hampered by financial problems with several star players quitting the club.
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