Yes — but they don't really set up shop in the ducts themselves.
Why they show up around vents
- Riding the air. Fruit flies are tiny and get pulled into return-air grilles from kitchens, fruit bowls, trash cans, drains, and the outdoors. You see them on the supply vent or near registers because the ductwork delivered them.
- Moisture sources at the air handler. They'll hang out at the indoor coil's condensate pan, around a leaky drip line, or where mold / organic slime has built up on an evaporator coil or a dirty blower compartment — that's the closest thing to a "nest" in the system.
Why the ducts themselves are a bad home
- Too dry. Standard sheet-metal or flex ductwork stays dry; fruit flies need moist organic film to lay eggs (think fruit, drains, mop buckets, damp mop heads).
- No food. A thin coat of dust and lint isn't enough to support a breeding population — they're not fungus gnats.
- Airflow. Eggs and larvae need a stable wet surface; constant moving air works against them.
What actually fixes it
- Get rid of the source, not the duct: ripe fruit, garbage, recycling, compost, and floor drains (pour boiling water or an enzyme cleaner down infrequently used drains weekly).
- Clean or replace the air filter so you're not just chopping up flies and blowing bits into the coil.
- If a fly keeps appearing at one specific register, have a tech check the condensate pan and evaporator coil for biofilm and standing water — that's the place in the system that's actually hospitable.
So: they can pass through the ducts, and they can breed on the wet evaporator/condensate side of the air handler, but the ductwork itself isn't where you'd expect an infestation.