Soren Schroder, Bunge's chief executive officer since 2013, will resign once a successor is named to his leadership post.
"We are making solid progress, and it is the right time to turn over the leadership reins," he said.
"The company has a strong legacy and an exciting future ahead."
The US-based company has set up a search committee to find his replacement.
The decision is in reaction to pressure from activist investors looking to improve Bunge's performance after stalled talks to merge with Glencore and ADM, Bloomberg has reported.
Kathleen Hyle, a board member since 2012, has become chairwoman while prior chairman L. Patrick Lupo remains a board member.
Hyle will serve on the CEO search committee with board members Paul Fribourg, J. Erik Fyrwald and Mark Zenuk.
Schroder, 57, joined Bunge in 2000 and has held a variety of agribusiness leadership roles, including chief executive of Bunge North America.
The company said his tenure included strengthening of Bunge's agribusiness and growth in food and ingredients, notably with recent acquisition of Loders Croklaan.
Hyle, 60, has served as the head of the Bunge board's Audit Committee for the past five years.
She has also served as senior vice president of Constellation Energy and chief operating officer of Constellation Energy Resources from 2008 until her retirement in 2012, when Constellation completed its merger with Exelon Corp.
Hyle joined Constellation in 2003, and served in a variety of senior-level finance and operations positions, including as chief financial officer of Constellation New Energy.
