Taking to social media, Nooyi shared some emotional posts with the people elaborating her time with the company and stated how she never imagined leading the company.
Nooyi will continue holding her chairman position through early 2019 to 'ensure a smooth and seamless transition, ' the company said in a statement.
The 64-year-old Nooyi has been with Pepsico for 24 years, and is a leading figure in an elite group of high-profile female CEOs.
Fortune credits Nooyi with moving PepsiCo's portfolio towards healthier fare: and PepsiCo has grown its portfolio of "Good for You" and "Better for You" options from about 38% of revenue in 2006 to roughly 50% in 2017.
Laguarta will take over from Nooyi on October 3 and will also join the board, the company said in a statement.
Nooyi, 62, will leave the CEO role on October 3.
She praised her successor, calling him "exactly the right person to build on our success". He is a terrific executive with a long and proven track record of growing businesses. I also want to thank Indra for her overwhelming support.
"Guided by our philosophy of Performance with goal - delivering sustained performance while making more nutritious products, limiting our environmental footprint and lifting up all the communities we serve - we've made a more meaningful impact in people's lives than I ever dreamed possible", she said.
He noted that, under Nooyi, PepsiCo expanded its portfolio of "Good for You" and "Better for You" options from about 38 per cent of revenue in 2006 to about 50 per cent in 2017, while simultaneously nearly tripling the company's investments in research and development to expand more nutritious offerings and minimize its environmental impact.
Meanwhile Laguarta, who has been with the company for 22 years, has been the president since September overseeing global operations, corporate strategy, public policy and government affairs at PepsiCo.
PepsiCo has delivered strong results under Nooyi's leadership.