Beneath the charming cobblestone streets of Cheesebridge, a posh Victorian-era town obsessed with wealth, class, and the smelliest of fine cheeses, dwell the Boxtrolls. The local residents see them as foul monsters who crawl out of the sewers at night to steal children and cheese.

In reality, the Boxtrolls are an underground community of quirky and lovable oddballs who wear recycled cardboard boxes. They find their necessities in dumpsters and by collecting mechanical junk. The Boxtrolls have raised an orphaned human boy, Eggs, since infancy as one of their own. When villainous pest exterminator Archibald Snatcher targets the Boxtrolls, hoping to get rid of them all in an effort to gain his his ticket into Cheesebridge society, the kindhearted band of tinkerers must turn to their adopted charge and adventurous rich girl Winnie to bridge two worlds amidst the winds of change.