Apple has long made the bulk of its products in China.
It avoided duties during Trump's first term after agreeing to invest more in America, in announcements that it coordinated with the White House.
But it has been scrambling since Trump launched a new tariff war in January, announcing an additional 30% levy on Chinese-made goods.
Apple has responded to changes by reworking its supply chain, shipping goods to the US primarily from India and Vietnam, which face lower tariffs on their exports.
But the company still paid out more than $800m in new border taxes on its products over the three months ended in June, reflecting Trump's sweeping global so-called reciprocal tariffs, which have been in place since April.
It is expecting to pay another $1.1bn in coming months, despite exemptions from the measures that the White House granted to certain electronics in April.
With tariffs on Indian-made goods now set to ramp up to 50%, it has raised tariff worries.
On a call with investors, Mr Cook emphasised Apple's involvement in the US, and its longstanding strategy of working with "third parties" to make investments.
He pointed to its previously announced plans to launch a "manufacturing academy" in Michigan, as well its pledge to buy $500m in rare earth magnets from MP Materials, which is working to expand production of rare earths in the US. The US government has taken a stake in that company as well, while committing to a minimum price for its output.
Since his return to office, Trump has often promoted high-profile commitments of investments by firms like Apple. Analysts say the numbers he uses often appear exaggerated and there is no evidence yet of a wider trend.
Paolo Pescatore, founder of PP Foresight, praised Mr Cook for deft navigation of Apple through "turbulent times" but said it remained to be seen what the investment would mean for the many different pieces that go into Apple devices and where they are produced.
"Certainly if you look at the case today, it's impossible to think now everything could just suddenly be produced, manufactured and put together in the US overnight," he said.