This paper presents an internally and globally consistent model of plate evolution in eastern Indonesia from Middle Miocene to Present time. It is centered on the Banda Sea region located in the triple junction area between the Pacific–Philippine, Australia and South–East Asia plates. The geological and geophysical data available from Indonesia were until recently insufficient to define a unique plate tectonic model. In this paper, the new data taken into account clearly restrict the possible interpretations. Owing to a great number of geological, geophysical and geochemical studies, the major plate boundaries (the Sunda–Banda subduction zone to the south, the Tarera–Aiduna Fault zone and the Seram Thrust to the east, and the Sorong Fault zone and Molucca Sea collision zone to the north) are now clearly identified. The age of the major tectonic structures is also better known. Geodetic measurements well constrain the Present time plate kinematics. We also consider the deformation history within eastern Indonesia, where numerous short-lived microplates and their related microcontinents successively accreted to the Asiatic margin. Moreover, magnetic anomalies identification of the North and South Banda Sea basins allows a precise kinematic reconstruction of the back-arc opening. We used the Plates software to test the coherency of our model, presented as a series of 4 plate reconstruction maps from 13 Ma to the present. Finally, the origin of oceanic domains restored by our reconstruction is discussed.