The executive, who steered the iconic brand through waning consumer interest in sugary drinks and added more than 10 billion-dollar brands, will be replaced by COO Henrique Braun.
The cookie took about four years to develop and is meant to "redefine what indulgence can look like," according to the brand's vice president of marketing.
The merger, the largest since Kraft Heinz's combination in 2015, would create a snacking giant with a portfolio including M&Ms, Snickers, Pringles and Pop-Tarts.
The technology, called AIDA, has cost the snacking giant more than $40 million so far, but the opportunity to produce ads faster and personalize them for consumers could pay off big later on.
The candy giant's chief customer officer said it is offering just 10,000 pistachio and kadayif-filled bars through GoPuff as a way to reach Gen Z consumers.
The Mondelēz chocolate chip cookie brand, with sales of approximately $1 billion and more than a 50% share of the category, is focusing much of its efforts on connecting with younger consumers.
The purchase of the better-for-you puffs and popcorn maker comes as the confectionery giant aims to grow its salty snacks division to 20% of revenue during the next decade.