After more than two decades at PepsiCo (NASDAQ:PEP), half of them as CEO, Indra Nooyi has resigned. Her exit from the beverage giant marks the end of an era, one investors ought to be happy is coming to a conclusion.

Although Nooyi's appointment was a groundbreaking achievement -- a minority female leading a Fortune 500 company is a rarity -- her tenure has failed where it matters most for investors: generating returns.

Two women drinking glasses of soda

Image source: Getty Images.

Losing its fizz

From October 1, 2006 -- when Nooyi stepped into the CEO role -- until the end of last week, shares of the soda and snack company gained only 73%, far short of the S&P 500's 112% rise.

Including the impact of dividends boosts Pepsi's total return to 141%. However, that also trails the S&P 500 on a total return basis and lags even further behind Coca-Cola (NYSE:KO), which generated a 194% total return over the same period.

PEP Total Return Price Chart

PepsiCo vs. Coca-Cola Total Return Price, data by YCharts.

Both Pepsi and Coke have suffered from a long-term decline in soda consumption, superseding any impact Nooyi could have made. Yet because Coke is a pure-play beverage company, it should have felt a much bigger impact than Pepsi. The latter's profitable Frito-Lay division, which makes snacks like Doritos and Lays chips, ought to have better captured the rise in snack food consumption.

A missed opportunity

Last November, market analysts at Nielsen noted that salty snacks and cookies and crackers were two of the fastest-growing snack food categories, each growing 6% over the previous year. Within the salty-snacks market, those foods that made health claims such as having no preservatives, being gluten free, or being organic achieved double-digit growth rates. (Non-GMO snacks saw the fastest growth, with a 29% annual increase.)

Although Frito-Lay North America hit $15.8 billion in sales in 2017, an 18% increase over 2010's $13.4 billion, that's less than 2.4% growth compounded annually.

The opportunity in snack foods led billionaire investor Nelson Peltz to try to split Pepsi up into two companies and use the snack food business to acquire global giant Mondelez International. Nooyi vociferously opposed this plan and ultimately won.

She also fought against other transformative deals, failing to make any big acquisitions. For example, she passed on the chance to acquire organic dairy producer WhiteWave Foods, which was eventually bought by Danone.

A chance for change

Missing out on WhiteWave was critical, because in turning away from soda, consumers were looking for healthy beverage alternatives. Earlier this year, Danone reported strong sales and improved profits, helped in part by integrating WhiteWave into its operations.

Nooyi did make acquisitions in the healthy snack food space, such as Pepsi's purchase of Bare Foods, a maker of baked fruit and vegetable snacks, that pushed further the outlook that the beverage giant's "better for you" snack business should maintain a higher profile. 

With Nooyi's exit, however, transformative deals may be back on the table again, as activist investors are sure to target incoming CEO Ramon Laguarta to make the changes his predecessor was loathe to do.

While any potential deal will need to be judged on its merits, Pepsi investors should be happy the torch has finally been passed, as there is now an opportunity for real progress to be made without a CEO standing in the way.

Rich Duprey has no position in any of the stocks mentioned. The Motley Fool has no position in any of the stocks mentioned. The Motley Fool has a disclosure policy.