Nick Bourne has resigned from Boris Johnson's government in protest at the prospect of a no-deal Brexit.
Lord Bourne, who had been a minister at the Wales Office and at the Housing Communities and Local Government department, said he had been asked to continue in both roles.
He said it is the first time he has resigned "in his life".
Lord Bourne was leader of the Conservatives in the assembly between 1999-2011.
The announcement came as new prime minister Boris Johnson continued to appoint ministers to his government on Friday.
Kevin Foster, MP for Torbay, has kept his junior ministerial jobs at the Wales Office and the cabinet office, and as a government whip.
Announcing his resignation, Mr Bourne tweeted: "I have resigned for the first time in my life and it is from a job which I really love and enjoy and which I had just been offered once more".
"But I cannot accept a no deal on 31 October and so I go," he added.
Lord Bourne served as Mid and West Wales Conservative AM until he lost his seat at the 2011 election.
On Friday Boris Johnson announced that his official title would include "minister for the Union" - a pledge he made during his leadership campaign.
A Downing Street spokesperson said this was a "statement of his commitment" to strengthening ties between the constituent parts of the UK.
Alun Cairns was confirmed as Welsh Secretary in Boris Johnson's cabinet earlier this week.