The squadron is the only MALS in 4th MAW with an active duty core of maintenance and aviation supply personnel.

In 1988, the unit was redesignated as Marine Aviation Logistics Squadron 49 with the headquarters located at NAS Willow Grove.

In February 1994 the MALS-49 flag was relocated from NAS Willow Groove to Stewart ANGB.

In 2024, the flag was relocated to MCAS New River, with supporting detachments established in JB McGuire-Dix-Lakehurst and NASJRB New Orleans respectively.

In 2004, the unit activated reserve Marines in support of Operation Iraqi Freedom to serve as augmentees for MALS-16 when they deployed to Iraq.