The tech giant is investing a "fair amount" into research and development, including "future stuff [he] can't talk about," the executive told shareholders. Cook didn't go into details, but lauded investors for thinking long term, especially Warren Buffett's Berkshire Hathaway.
Despite being one of the world's richest public companies, Apple's dearth of new blockbuster products has led some to wonder whether it is still innovative. Still, many on Wall Street say the company is investing heavily. UBS on Tuesday wrote that Apple "may have over 1,000 engineers working on a project in Israel that could be related to AR [augmented reality] ... the next major innovation from Apple."
The annual meeting gathered representatives of its 26,000 shareholders for mostly routine tasks like re-electing its board of directors, approving its accounting firm and signing off on Cook's $8.75 million annual compensation for 2016.
Also on the agenda were a series of proposals from shareholders who hold $2,000 of Apple's stock, which must be approved by a form of majority vote.
Shareholders like Rev. Jesse Jackson also pressed executives to speak up on current events affecting the technology industry. One example? The government's push to bring back manufacturing from overseas.
"We know that this company could never have thrived somewhere else, we love this country," Cook said, noting that two-thirds of Apple employees are in the U.S., and many components are built domestically.
But Cook said that focusing just on building the final product in the U.S. "discounts the reality" of the situation. He said Apple is not a big lobbying company, and doesn't "like politics," but playing a role in policy discussion is important.
(Apple's spending on lobbying has ticked up considerably under Cook's leadership, according to Opensecrets.org. Former Vice President Al Gore sits on the board.)
Another political issue that could affect Apple's burgeoning software and services business is net neutrality — the concept that internet providers can't discriminate between, or charge more for, more intensive types of content. The Trump administration may decide to let companies decide what to charge, which could make some of Apple's content more expensive to deliver.
Apple thinks content should be treated the same, and there should be no unfair advantage for one group over another, Cook said.
Other issues on the table Tuesday were the environment, privacy, diversity, human rights and the environment.
Cook said the company is working on "greening" its supply chain and is a "staunch defender" of privacy. Jackson said at the meeting he was grateful for Apple's stance on privacy, but pushed it on social "obligations" to minority groups.
Still, shareholders shot down proposals to alter diversity hiring practices or ramp up disclosure on charitable giving.
— Reporting by CNBC's Josh Lipton and Megan Hawkins