The screenwriters for Star Trek, Roberto Orci and Alex Kurtzman, are already working on a sequel and at the San Diego Comic-Con this past weekend, Orci was able to share that the sequel might be only the beginning of a two-movie storyline:
Nothing was decided [at the last meeting] ... [The studio said to us] "We thought maybe you could do that as like 2 and 3."
Two-part storylines are not unusual in the Star Trek universe, with Star Trek II: The Wrath of Khan wrapping up in Star Trek III: The Search for Spock. While Orci doesn't give a lot of details away, clearly he and Kurtzman have something big in mind for the next Star Trek.