Trott first took charge of the Asian side in July 2022 and has overseen the team's rise as a formidable white-ball side.
Afghanistan beat England, Pakistan and Sri Lanka and came close to toppling eventual champions Australia at the 2023 ODI World Cup in India.
They also reached the semi-finals of a global tournament for the time at the 2024 T20 World Cup.
The 2026 T20 World Cup, which is likely to be held between February 7 and March 8 in India and Sri Lanka will be Trott's last assignment with Afghanistan.
The former England international said: "It has been a privilege to work with the Afghanistan National Team and to witness their passion, resilience, and hunger to achieve greatness.
"I am proud of what we have accomplished together, and I will always remain a supporter of Afghan cricket. I wish the team and the Afghan people continued success in the years ahead."
The ACB said in a statement: "ACB recognises that coaching transitions are a natural part of the global cricketing ecosystem. Just as teams evolve, so do their leadership and strategic needs.
"No international side remains under a single coach forever, and this change marks a new chapter for Afghanistan as the board continues building toward long-term excellence.
"This decision comes as part of ACB's long term strategic planning for the next phase of the national team's growth."
Richard Ngarava took five wickets in the second innings as Zimbabwe completed an innings and 73-run victory against Afghanistan on the third day of the one-off Test played in Harare.
Zimbabwe will host Afghanistan for a one-off Test match and three T20Is, starting later this month, the African country's cricket board has confirmed.
Pakistan batter Babar Azam has been dropped for Pakistan's upcoming Asia Cup tournament against the UAE and Afghanistan, alongside Mohammad Rizwan, while Fakhar Zaman misses out through injury.
Afghanistan kept their Champions Trophy semifinal hopes alive with a thrilling eight-run victory over England in Lahore on Wednesday.
