Earlier, the space agency released the most detailed picture yet as it hurtled towards the dwarf planet on Tuesday.
The probe was set to grab more images and other data as it passed just 12,500km from the little world at 11:50 GMT (12:50 BST).
The spacecraft is currently out of contact with Earth as it continues its observations.
Talking about the latest image of Pluto that was returned just before the flyby, Nasa’s science chief, John Grunsfeld, said: “This is true exploration… that view is just the first of many rewards the team will get. Pluto is an extraordinarily complex and interesting world.”
Dr Stern said: “On the surface we see a history of impacts, we see a history of surface activity in terms of some features we might be able to interpret as tectonic – indicating internal activity on the planet at some point in its past, and maybe even in its present.
“This is clearly a world where geology and atmosphere – climatology – play a role. Pluto has strong atmospheric cycles. It snows on the surface. These snows sublimate – (and) go back into the atmosphere – every 248-year orbit.”
The probe is investigating not only Pluto but also its five moons: Charon, Styx, Nix, Kerberos and Hydra.
To achieve that, it has had to perform a furious set of manoeuvres during the flyby, pointing every which way in the sky to lock on to the different targets.
Al Tombaugh (son of the man who first found Pluto) is obviously delighted that a sample of his father Clyde’s ashes is on board New Horizons, speeding past Pluto and now heading into the unexplored realm of the Kuiper Belt.