Former Managing Director of the company, Sanjiv Khanna will succeed him.
Nagarajan, who has been leading Mother Dairy Fruit & Vegetable Pvt Ltd as the Managing Director since May 2010, will continue in this role only till June 30.
"I had put in my papers in March due to personal reasons. I want to spend time with my parents who live in Bengaluru," he said when contacted.
His resignation was accepted by the company's board in its meeting held on June 13.
Under his leadership, Mother Dairy scaled up its operations with the launch of various products and variants, widening its offerings.
His successor Khanna is currently serving as CEO of SBC Beverages Ghana.