Cooper Union President Jamshed Bharucha announced his resignation Wednesday evening following months of trustee infighting amid a state probe.

Mr. Bharucha said he would leave at the end of June after four years as president and would serve as visiting scholar at Harvard University in the Graduate School of Education in the fall.

“The focus of my presidency has been to secure Cooper’s finances for generations of deserving students in the future, while preserving excellence and increasing socio-economic access,” he said in an email to faculty.

Mr. Bharucha’s anticipated departure had already made waves this week: Five trustees who support him resigned in unison on Tuesday.

The shake-up in the 23-person board comes at a tense time for Cooper, formally named the Cooper Union for the Advancement of Science and Art. Last year, New York Attorney General Eric Schneiderman began probing the board’s financial moves, following the Manhattan arts-and-engineering school’s decision to begin charging undergraduate tuition in 2014 for the first time in its history.