Despite the lower-than-expected unit sales, Cook told CNBC that the iPhone 7 Plus sales were "extremely strong."
"We are having significant growth rates beyond what we ever dreamed of," Cook said.
Services revenue rises 18 percent year over year
Meanwhile, Apple has invested in new content, like a Tribeca Film Festival movie, for Apple Music. It's part of a growing source of revenue for Apple, services, which includes digital content, AppleCare, Apple Pay, licensing and other services.
"In services, the App Store was up 40 percent and our developer community is growing by over 20 percent. There is a lot of momentum," Cook told CNBC.
Cash pile hits $256.8 billion — and tax rate forecast to fall to 25.5 percent in fiscal Q3
Apple's massive cash hoard could become a major windfall for the company under the new presidential administration, which campaigned to cut taxes on the repatriation of cash held overseas.
Cook told CNBC a rate between 6.5 and 10 percent "seems rational" for a one-time tax holiday on foreign-earned income.
China sales fall 14 percent from last year
Apple's biggest Asian revenue source has been under pressure, as the strength of the Hong Kong dollar dampens shopping from mainland China. Sales fell 12 percent year over year last quarter.