During the Plio-Quaternary, the Bonaparte Basin is characterized by a very wide (> 600 km, > 370 mi) carbonate platform and 200 km-wide (125 mi-wide) intra-shelf basin (the Malita ISB). Using 3D and 2D seismic data combined with exploration well data, this study characterizes the stratigraphic evolution of the Malita ISB during the last 3.5 million years. Two third-order transgressive sequences can be distinguished. A late Pliocene transgression occurred over an irregular topography resulting from the flexural reactivation of the Malita graben. In the centre of the intra-shelf basin, carbonate aggradation resulted in the formation of isolated carbonate platforms separated by deeper water seaways and inter-platform areas. Wider and more numerous carbonate platforms developed on the edges of the intra-shelf basin. During the late Quaternary, renewed flexural deformation initiated a second transgressive cycle marked by higher subsidence rates in the ISB centre than along its edges. High rates of accommodation creation (at third-order) combined with higher-frequency (fourth-order), high-amplitude fluctuating sea levels and increased clastic input resulted in the progressive demise and burial of the carbonate platforms in the ISB centre. Thus, the Plio-Quaternary stratigraphic architecture of the Malita ISB is strongly controlled by differential subsidence that controls spatial distribution of accommodation and ultimately platforms architectures.The Malita ISB constitute a rare recent analogue for Paleozoic and Mesozoic hydrocarbon-bearing intra-shelf basins.