Some unrenumbered 16 class units were also transferred to freight service and were used mostly on branchline trains in Kansas and Texas until the last one was retired in 1972. After Amtrak stopped using the 300 class F-units between January and July 1973, the surviving operational units were also transferred to freight service and were renumbered into the 325 class in September.

When the 325 class was transferred to strictly freight service after Amtrak took over passenger operations, the Santa Fe decided to give them a freight color paint scheme. The first few repaints featured a blue warbonnet on A-units in place of the former red on the silver carbody and a blue stripe along the lower carbody on B-units. Seven A-units (325,327,329,332,335,338,and 343) and several B-units received the bluebonnet scheme. The blue scheme was apparently not well received and subsequent units were repainted with yellow warbonnets. Most of the remaining 325 class units received the yellow scheme before going into the CF-7 rebuild program, but 342L became the last A-unit to operate in the clasic red warbonnet passenger scheme and it went to the CF-7 program still wearing red.