Carbonate depositional models are often informed by the study of platforms of good lateral continuity and sizable thickness, because of their significance in petroleum geology. However, spatially restricted and more ephemeral carbonate accumulations can be an important but frequently overlooked component of otherwise siliciclastic-dominated or mixed carbonate–siliciclastic systems. Pliocene successions of Tuscany and the Tyrrhenian shelf (Northern Apennines, Italy) record a regional pulse of nontropical carbonate deposition across several restricted basins that has not yet been precisely constrained in its genesis and correlation. This study investigates the stratigraphic expression of these carbonates to extract general aspects applicable to carbonate sedimentation across tectonically structured and physiographically complex shelves. Analyses of the extension, composition, facies, and sequence stratigraphic architecture of the studied Piacenzian carbonate units are complemented by new biostratigraphic and magnetostratigraphic data, which document the slightly diachronous development of the carbonates within Mediterranean planktonic foraminifera Subzones MPL4b and MPL5a and magnetic polarity Chron C2An. The carbonate units are part of a regionally defined, tectonically controlled sequence, and represent the first transgressive unit overlying the basal sequence boundary, but are also found in the regressive portion of the sequence. Collectively, the units document the establishment of a shallow-marine carbonate factory, dominated by calcareous red algae, the larger benthic foraminifer Amphistegina, and heterozoan skeletal components, along the margins of a complex, archipelago-like coastal domain. A review of the studied successions and other examples from the literature indicates that carbonate accumulations in settings with varied coastal physiography and active partitioning of depocenters are generally characterized by: a) spatial discontinuity; b) an overall skeletal association consistent across separate basins, but with local variability in dominant skeletal components; c) preferential accumulation along basin margins or over isolated structural highs not in direct proximity to a hinterland with major drainage systems; d) predominance of low- to moderate-energy facies; e) preferential onset of deposition during transgression, with possible development of mixed carbonate–siliciclastic facies; and f) differing internal stratigraphic architecture tied to the specific subsidence and uplift history of coeval individual basins. These observations built upon the study of mid-Piacenzian carbonate units from the central Mediterranean contribute to the refinement of carbonate facies models and their application in the fields of sequence stratigraphy and basin analysis.