Symbiosis
The plants can't easily concentrate helium from the atmosphere, because it interacts pretty weakly with most things, and it is so small it can slip straight back out of most enclosing membranes. Think of what happens to the helium balloon you might save from a fairground.
The plants also can't easily extract helium the way people do, because it comes from a natural gas well, tapping underground domes where it accumulates like the methane. (See Wikipedia) Plants aren't great at drilling natural gas wells.
Fortunately, your plant has a long-standing symbiotic relationship with a type of fungal mycelium that is capable of boring to great depths by secreting potent acids. That mycelium takes up natural gas to react at the surface for a well-nigh endless supply of energy. It also allows a steady stream of helium to diffuse through its tissues to the surface.
Your plant airdrops its fruits onto outcrops of these mycelia. The fruits supply nutrients including trace minerals from far away, dissolving into a sticky membrane that covers the happy fungus. The membrane traps helium emitted by the fungi, thinning and shaping itself into a balloon. When the time is right, the new balloon plant soars away with its captured gas.
Note: using hydrogen or methane seems much more sensible, but why should we cave in to that?