PepsiCo's worldwide operations rely less on beverages and more on snacks, an area Nooyi is largely credited with re-shaping and expanding as consumers shifted away from sodas and focused on healthy foods.
She was promoted to CEO in 2006, not long before the mortgage crisis-fueled Great Recession.
Here are some of her most inspirational quotes on leading as a woman.
And as she steps aside, the company is highlighting her strong financial results.
Since the middle of previous year, several high-profile female CEOs have announced they were stepping down, including Marissa Mayer at Yahoo, Irene Rosenfeld at Mondelez and Meg Whitman of Hewlett Packard Enterprise.
"This company has been my life for almost a quarter century and part of my heart will always remain here", Nooyi said in a prepared statement.
On a corporate level, Herzog said the announcement was not a surprise and could herald strategic shifts for PepsiCo in the near future, including refranchising with regional bottling partners or dividing the company.
He previously headed Europe Sub-Saharan Africa division - a unit PepsiCo characterized as "one of the most complex business divisions in the company".
Nooyi, who is from India, is the first foreign-born CEO of Pepsi and the first woman to lead the chips-and-soda behemoth, whose revenue topped $63 billion past year.
Since being appointed CEO in 2006, Nooyi engineered a balanced portfolio of food and beverage products labeled either "better for you", "fun for you" or "good for you".
During her dozen years at the helm, Nooyi led PepsiCo's transition from a seller of sugary soft drinks and sodas and fatty foods to a greener more health and environment conscious company even at the risk of hurting its bottomline, although some critics saw her effort as inadequate.
Still, Pepsi's stock lagged the broader market in recent years, and it has trailed rival Coca-Cola. Both Coke and the S&P also have slightly outperformed Pepsi during Nooyi's tenure.
Shares are up in early trade, at around 1.25%.
Reminiscing about the time spent and work done in the company for several years, she also tweeted about the work she is proud of.
The Frito Lay snacks business now contributes 46 percent in total operating profits, almost double its beverage business. Among PepsiCo's brands are Mountain Dew, Tropicana, Gatorade and Quaker Oats.