This paper explores variability in cave use in central Maluku from initial settlement in the late Pleistocene to the ethnographic present. Significant variability exists. Historic and ethnographic accounts highlight cave use that is not often considered by archaeologists. Some uses may leave few archaeological signatures. Factors affecting different cave uses are examined, including environmental, social/cultural, and historical factors. The effects of immigrant population influences, such as the Austronesian immigration into and/or influence on central Maluku, are also important considerations. The possibility of multiple migrations of pre-Austronesians and various Austronesian groups, and the subsequent effects on cave use, are also discussed. Archaeological case studies include the Labarisi site (north Buru), the Hatusua site (southwest Seram), and several cave sites on the northern Leihitu Peninsula (Ambon).