In November 2017 it was reported that Elphicke had been suspended from the Conservative Party after "serious allegations" made against him were referred to the police. Elphicke stated: "I am not aware of what the alleged claims are and deny any wrongdoing.". His wife, Natalie Elphicke, immediately defended him, asserting that the manner of his suspension was a threat to British values and an injustice.
In March 2018 Elphicke was told that he was accused of sex offences against two members of his staff. He said in response: "I am completely confident I will be able to prove my innocence." In April 2018, The Sunday Times reported that a rape allegation had been made against Elphicke in November 2017, at the height of the Westminster sex scandals, but that the police had not informed him of it for about five months.
After The Sunday Times published its report that Elphicke was under police investigation, he sued in order to shut the story down, using libel and privacy laws. The woman who accused him of raping her in 2015, referred to as 'Jane', said this had prolonged her suffering. Following his conviction in 2020, he withdrew his claims in March 2022, and the newspaper published more detail about the events.
On 12 December 2018 Elphicke had the Conservative whip reinstated prior to a confidence vote in Theresa May.
On 22 July 2019, the Crown Prosecution Service (CPS) announced they had charged Elphicke with three counts of sexual assault relating to two women: one charge relating to an incident in 2007 and the other two in 2016. He appeared at Westminster Magistrates' Court on 6 September 2019 and denied all three charges. In their statement, the CPS emphasised that Elphicke "has a right to a fair trial" and that "there should be no reporting, commentary or sharing of information online which could in any way prejudice these proceedings". The Conservative Party again withdrew Elphicke's whip later that day. In October 2019 Elphicke appeared at Southwark Crown Court and was granted bail to return for trial on 29 June 2020.
During his trial the court heard how Elphicke groped one of his accusers, chased her around his house, and sang "I'm a naughty Tory, I'm a naughty Tory." On 30 July 2020, Elphicke was found guilty on three counts of sexual assault. On 15 September, he was sentenced to two years in prison. He sought leave to appeal against the sentence, but this was denied in March 2021.
He was released from HMP Leyhill in Gloucestershire on 14 September 2021 after serving half of his sentence. He was summoned back to magistrates court for non-payment of the £35,000 costs order awarded at his original trial; he claimed to be unable to pay, stating that “I have no job, I have no career, I am long-term unemployed,” and that he was living in a rented one bedroom flat and claiming Universal Credit. He was nonetheless ordered to pay £35,000 within a year towards the costs of the prosecution. In April 2022, Sky News reported that Elphicke was struggling to find new employment.
A campaign to present Elphicke as a victim was joined by several individuals, including the parliamentary whips who rescinded his suspension in December 2018, and his wife, Natalie. She and four other MPs (Sir Roger Gale, Theresa Villiers, Adam Holloway and Bob Stewart) were obliged to apologise or be suspended from the Commons for improperly trying to influence a judge, when they had signed a letter on parliamentary notepaper to the Lord Chief Justice pressing Mrs Justice Whipple not to disclose character statements in his trial at Southwark.