Charlie Elphicke, who has represented Dover since 2010, lost the Tory whip in 2017 when the allegations were referred to the police.
He was readmitted to the party in December prior to a confidence vote in Theresa May’s premiership, but was again suspended when he was formally charged in July this year.
His wife, Natalie, was formally selected as the candidate for his Kent seat on Friday, after being voted in by local members.
Mr Elphicke is accused of a sexual assault against one woman in 2007 and two assaults against a different woman within a week of each other in 2016. He denies the allegations and has stood down to fight them in court.
Describing his tenure as an MP as the “greatest honour and privilege of my life”, Mr Elphicke said: “I am standing down today with huge regret, because it seems that we no longer abide by the basic British value of an individual being deemed innocent unless and until proven otherwise in a fair trial.
“That sacred principle of our national life has been sacrificed in the current climate – as became clear with the false pursuit of baseless allegations against high profile individuals, some of whom were smeared beyond the grave.
“In my case, I have been subjected to daily falsehoods and vile abuse – from the malfeasance of cabinet ministers to the malice of Twitter trolls.
“This has had the cumulative effect of jeopardising my right to a fair trial on charges I know to be baseless.
“That is why, having continued to work tirelessly for my constituents since these allegations were first made two years ago, I have now decided to stand down at this election.”
Mr Elphicke retained the Dover seat in 2017 before briefly losing the Tory whip, receiving 27,211 votes to Labour’s 20,774.
Ms Elphicke, who works as chief executive at the Housing & Finance Institute and reportedly volunteers at a local night shelter, said she was “delighted” to have been adopted as the constituency’s Tory candidate.
“Our Conservative team has achieved so much since 2010 – and I am looking forward to building on these tremendous achievements,” Ms Elphicke said.
“I will fight tirelessly to deliver better healthcare, more jobs and money, better schools, high quality affordable housing, more police on our streets – and stronger, more secure borders.”
Dover and Deal Conservatives Association chairman Keith Single said: “We considered matters most carefully and it is clear to us that Natalie will be an outstanding candidate for the Conservatives in Dover & Deal.
“She has loyally and effectively campaigned for the Conservatives over the past 30 years, and with us in Dover and Deal for over a decade. Nationally, she has led a government review into housing policy and been director of the Conservative Party’s policy forum.
“Her expertise in national policy combined with her experience of local constituency issues makes Natalie a first class Conservative candidate.
Additional reporting by PA