Yes, it will
Ongoing spell effects are not part of a creature's statistics, so they are not replaced when the creature is polymorphed, and not un-replaced when polymorph ends.
Feeblemind is a bit tricky, because it has a duration of Instantaneous, and normally the effects of instantaneous spells are permanent and non-magical, so normally it would only set the beast's Intelligence to 1 (whatever it was before), and when the beasts stats go away, that Intelligence of 1 also would.
However, feeblemind says:
At the end of every 30 days, the creature can repeat its saving throw against this spell. If it succeeds on its saving throw, the spell ends.
This effect is more specific than the general rule, and overrides it. Feeblemind creates an ongoing spell effect, and that effect will stick to the creature when polymorph goes away, until it makes its save. Since the main effect of feeblemind is
On a failed save, the creature's Intelligence and Charisma scores become 1. The creature can't cast spells, activate magic items, understand language, or communicate in any intelligible way. The creature can, however, identify its friends, follow them, and even protect them.
And since it is still the same creature that failed the save (just with different stats), this effect will continue to set its Intelligence to 1.