Matheson, who has served in various ministerial roles in Scotland’s devolved government over the last decade, said it was “in the best interest of myself and the government for me to now step down”.
A Scottish Parliament probe into the matter is due to conclude in the coming weeks, but the Scottish National Party (SNP) lawmaker said he was quitting so it “does not become a distraction”.
The scandal erupted last November after it emerged Matheson had incurred a bill of nearly £11,000 (Ksh.2.2 million) on his government iPad while on a family holiday to Morocco.
He initially insisted the eye-watering charges had been run up while he was using the device for official business during the trip, that began in late December 2022.
But he then backtracked, admitting his teenage sons had used it to watch football.
The U-turn came after opposition parties pointed out that he would have had to send some 8,000 emails in 24 hours to incur a £7,300 bill on one of the days.
Matheson claimed at the time that he “did not knowingly run up the roaming charges bill” and had reimbursed the money in full, which had originally been paid by the Scottish Parliament.
Scotland’s First Minister Humza Yousaf said last November he had “absolute confidence” in Matheson as a minister and that “honest mistakes do happen”.
Welcoming his resignation, opposition parties said Thursday that the saga also reflected badly on Yousaf.
“The first minister has big questions to answer over his lack of judgment,” Scottish Labour deputy leader Jackie Baillie said.