Louis Stedman-Bryce, who was elected six months ago, said he would sit as an independent MEP.
Last week Mr Stedman-Bryce announced he was quitting as a general election candidate for the Brexit Party in Glasgow North East in protest at Nigel Farage’s decision to stand down his candidates in all 317 seats the Conservatives are defending.
In a video posted to twitter, the MEP said: “This week it saddens me further to say that I’ve taken the decision to leave the Brexit Party.
“This is because I find myself in a situation where my personal values are now in direct conflict with those of the party.
“And this for me is an area where I cannot and will not compromise.
“Almost a quarter of a million people in Scotland voted for the Brexit Party to represent them here in the European Parliament and to ensure that Scotland had a voice in the Brexit debate.
“But unfortunately I feel the party has repeatedly failed to deliver on either of those promises.”
On Monday, the Brexit Party withdrew support for its candidate in the Fife constituency of Glenrothes after he was accused of “rampant homophobia”.
In a Facebook post to an account in his name, evangelical pastor Victor Robert Farrell wrote in 2017: “Western nations look at your hands. Young lesbians in parliament, old lesbians leading political parties. Perverts pushing sodomite rights. The aged living in fear.”
A Brexit Party spokesman said: “The Brexit Party does not share these views. We have withdrawn our support for the candidate.”
Mr Farrell did not respond to The Scotsman’s request for comment.
“Whilst the Brexit Party’s position on Brexit may have changed, mine has not, and I remain committed to Brexit and to the people of SCotland who voted for me and I will fight on unhindered as an independent MEP to ensure our voice is heard.”
A Brexit Party spokesman said Mr Stedman-Bryce was an "amazing man" and that the party was "sorry to lose him". In relation to Mr Farrell's homophobic comments, the spokesman added that "within minutes of this fact emerging we severed ties and funding with the individual".