The mystery of how nearly $5 million in diamonds went missing from a Midtown jewelry store has been solved.

As it turns out, some dimwitted workers at J. Birnbach Inc. were helping their boss move to another floor and tossed three weathered wooden boxes filled with diamonds in a heap of trash without bothering to look inside, law enforcement sources said.

But a building security guard patrolling the third floor allegedly did take a peek — and discovered the mother lode: a cluster of expensive stones, including one worth $3.2 million.

Wilfred Martinez, 47, sold some of the booty to a jeweler in the same building where he found them, but not the 17-carat diamond that was the $3.2 million crown jewel of the collection, the sources said.

He has now turned over that piece to cops, along with two smaller diamonds and $10,000 in cash.

Authorities are trying to track down the rest of the stones, law enforcement sources said.

Cops reviewing surveillance video from Nov. 24 saw Martinez grab the boxes from the third-floor hallway, and arrested him at 4 p.m. Monday at the building on Fifth Avenue and 47th Street.

He has been charged with criminal possession of stolen property. Judge Melissa Crane set his bail at $100,000 at his arraignment in Manhattan Criminal Court on Tuesday.

Jeweler Jonathan Birnbach initially told cops he tucked the three boxes away in a safe that had been left unlocked on Nov. 24, and didn’t discover the gems were missing until last Wednesday.

Additional reporting by Reuven Fenton and Larry Celona