During the Pliocene–Quaternary, the Bonaparte Basin is characterized by a very wide (>600 km [>370 mi]) carbonate platform and 200-km-wide (125-mi-wide) Malita intrashelf basin (ISB). Using three-dimensional and two-dimensional seismic data combined with exploration well data, this study characterizes the stratigraphic evolution of the Malita ISB during the last 3.5 m.y. 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 center of the ISB, carbonate aggradation resulted in the formation of isolated carbonate platforms separated by deeper water seaways and interplatform areas. Wider and more numerous carbonate platforms developed on the edges of the ISB. During the late Quaternary, renewed flexural deformation initiated a second transgressive cycle marked by higher subsidence rates in the ISB center 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 center. Thus, the Pliocene–Quaternary stratigraphic architecture of the Malita ISB is strongly controlled by differential subsidence that controls spatial distribution of accommodation and ultimately platform architectures. The Malita ISB constitutes a rare recent analogue for Paleozoic and Mesozoic hydrocarbon-bearing ISBs.