Cobbler arrived at Key West 11 January 1946, for operations locally and in the Caribbean for exercises and training until 27 November 1948.

She then sailed for Groton, arriving 1 December for a GUPPY II modernization being completed on 17 August 1949.

Her operations in the Caribbean and off the east coast continued, until 6 January 1958, when she departed Norfolk for a tour of duty in the Mediterranean Sea, returning 18 April.

She resumed operations off the east coast, cruising to Bermuda in June 1958, and to Quebec with midshipmen embarked in July 1959.

She had a 15-foot (4.6 m) hull extension added forward of the control room, a plastic sail and the BQG-4 PUFFS passive ranging sonar, which included the three sharkfin sensors on her deck.