A person entered the bank on Plaza Boulevard in National City wearing a dark blue hoodie with only eyes showing.
The person dropped off two packages - one red and one green - then left the building.
Soon after, the bank received a call from an unidentified man telling employees to put $100,000 in the red package or the green package would explode, police said.
Witnesses reported seeing a person fitting the clothing description running west of the bank location. The person took off the clothing and continued to run according to police.
Something suspicious may have been left under the clothing officials said.
The bank was evacuated along with 25 to 30 businesses in the South Bay Plaza Shopping Center.
A robot was sent into the building to examine the packages to see what type of device, if any, may be inside.
Keep up to date on breaking news: Follow us on Twitter @nbcsandiego, fan us on Facebook, sign up for our breaking news e-mail alerts or text SDBREAKING to 622339 to receive text messages for local breaking news. (Standard rates apply)