Firearms officers from the Met Police carried out a stop on a car in High Street shortly before 20:00 GMT on Wednesday.
Two men in their 20s were arrested on suspicion of possession of a firearm and possession of ammunition.
The operation was not linked to a fatal police shooting at Tracey Court in Luton earlier in the day, police said.
Detectives from the Met's serious and organised crime command were supported by officers from Bedfordshire Police during the operation.
Local residents were warned by armed police to stay inside their homes during the incident.
The arrested men are being held in custody at a police station in north London.
A handgun and ammunition have been seized and two people were arrested during a police operation in Luton.