The South African, appointed in 2022, oversaw a period in which Ireland qualified for three consecutive T20 World Cups, secured their first three test match victories, and claimed their first-ever series win against India.
Few gave Ireland a chance in the two-match series, but they humbled India twice in three days, spoiling Shreyas Iyer's debut series as India's 20-overs captain. It was India's first T20 series defeat since 2023.
The 45-year-old's current contract extends into early 2027, but Cricket Ireland said in a statement: "He (Malan) believes the timing is right in the cycle to step back following the just-concluded successful T20 series versus India."
Malan will be replaced by Gary Wilson, who represented Ireland 292 times as a player between 2005 and 2020. Wilson joined Ireland's coaching setup as assistant coach in 2022, and becomes the first Irish-born head coach in over 30 years, following John Wills in the early 1990s.
"It has been an absolute privilege to work with these players, staff and the wider Irish cricket community," Malan said in a statement.
"On the field, we can look back with great pride," he added, pointing to a T20 World Cup victory against England, Ireland's first-ever Test victory against Afghanistan and a first home Test win vs Zimbabwe among the highlights.
Malan will work alongside Wilson over the coming month to ensure a smooth transition as Ireland prepare for a one-day international series against Afghanistan in August.
Cricket Ireland also said that the transition will allow Wilson to use the upcoming ODI series as part of the preparations towards the World Cup qualifiers early in 2027.