The suspect threw a rock through one of the windows of the store at 2217 South Shore Center at about 9:45 p.m. and went inside, according to Alameda police Sgt. Don Owyang.
The suspect approached the store's manager at a kiosk, exposed a black semi-automatic pistol and demanded cash, Owyang said.
After receiving two cash register drawers' worth of money, the suspect left without firing any shots, according to Owyang.
The suspect is described as a black male wearing dark clothes and possibly a ski mask and gloves, Owyang said.
Police believe Wednesday's robbery may be linked to robberies at two other Trader Joe's stores in Walnut Creek and El Cerrito this summer. The Walnut Creek robbery occurred Saturday night.
"They're fairly similar as far as operation and suspect description," Owyang said. He pointed out that each robbery happened after closing and involved a black male suspect armed with a handgun.
Anyone with information about the robberies is asked to call Alameda police at (510) 337-8350.