A man being questioned in connection with a fatal Madison Avenue jewelry-store robbery had a bulletproof vest in his apartment and a safe filled with stolen gems — including a necklace from the robbed shop, sources said.

Police had yet to charge the man last night, but spent nearly 24 hours quizzing him at the 19th Precinct station house about the $1.2 million heist, in which an elderly employee was shot to death.

Cops also recovered clothes from the man’s Washington Heights apartment, and will test them for blood and DNA evidence that could link him to the crime. Henry Menahem Z”L, 71, was shot in the chest on Jan. 28 when a masked bandit entered R.S. Durant Jewelers on Madison Avenue on the Upper East Side. Police said the gunman entered the shop, threw two canvas bags at Menahem and a co-worker and demanded they fill them up.

When both men refused, the robber released an ammo clip from his 9 mm semiautomatic handgun, showed them the bullets and yelled, “You think I’m kidding? This is real.” Then he fired a single bullet into Menahem’s chest.

The co-worker begged the gunman to let him call 911 and save Menahem, but the killer cruelly said “no,” and continued to grab the loot.

The thief made off with about 700 gems. The haul was so heavy that the crook had to ditch a box containing a Fabergé egg.

Detectives recovered nine of the 66 pieces stolen during the heist. The recovery led them to the Washington Heights apartment, where they also found cash and some jewels, including the necklace, sources said. The stolen items include a $105,000 diamond necklace, a $75,000 ruby-and-diamond necklace and a $65,000 diamond necklace.