The Reverend Dr Paul Overend is accused of grabbing a woman and kissing her at a party while he was a chaplain at Cardiff University in 1997.
Reverend Canon John Patrick told BBC Radio Lincolnshire that the ongoing investigation had an impact on his decision.
He said: “We are all subject to the world in which we live and whether that’s in a relationship, in a family or community what’s happening around us affects the decisions that we make.
“I think you’re always looking at what God is calling you to do and it’s not something that has happened overnight.
“This is a decision that I’ve been working on for quite a long time and God calls you to different places. I feel this is the right time for me to be called to do something different.
“While there have been, undoubtedly, challenges along the way, it has been wonderfully rewarding to be a part of the cathedral community.
“I treasure the time that I have spent here and the friendships made.”
The Lincolnite approached Lincoln Cathedral for a comment on the latest departure, but nobody was available at the time of writing.
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A Lincoln resident is frustrated with vehicles parking on single yellow lines on Lincoln High Street, while the county council says the current regulation order means it’s unable to enforce the area properly, despite signage saying cars cannot park there.
Richard Bridgen has been living off Riverside Drive in Lincoln for around five years now, and over recent months he has noticed a particular trend around parking on a section of the High Street, which can impede his view as he tries to turn from Gaunt Street.
Lincoln residents in the Boultham area have become increasingly hesitant to report crime, citing concerns that the shortage in police staffing will lead to a lack of response.
Lincolnshire County Councillor Kevin Clarke (Labour) reports being contacted by multiple residents in the last few months who have suffered break-ins at their homes or gardens. Despite these incidents, they claim to have received minimal support from Lincolnshire Police.