The incident took place at the Island Savings credit union in the Victoria suburb of Langford at about 11:30 a.m.
Police say a suspect wearing a black balaclava entered the credit union, produced a firearm, demanded money and fled in a car with an undisclosed amount of cash.
But a witness recorded the licence-plate number and investigators were able to locate the vehicle at a local residence.
Police say members of the emergency response team were called in because a firearm was involved.
The name of the suspect has not yet been released, but police say he is known to them and lives locally.