Here we report the results of excavation and analyses of an open site on Pulau Ay, a small (ca. 4 km2) limestone island located in the Banda Islands, central Maluku, Indonesia. This report provides results of excavations at PA1 and other Pulau Ay sites conducted in 2007 and 2009. These sites reveal patterns of changes in marine resource exploitation, pottery, and use of domestic animals, particularly between initial occupation of the site at approximately 3500 b.p., and later phases commencing approximately 3000 b.p. Archaeobotanical analyses reported here provide insight into early Neolithic plant use, including early use of Myristica fragans (nutmeg) in a food context. The PA1 site adds to a growing data set about early Neolithic lifeways in Island Southeast Asia and provides a new view of cultural adaptations happening in the region during this critical period.