Alkaline carbonate-rich systems may, under some circumstances, result in significant accumulation of aqueous phosphorus. Additionally, the geochemistry of modern alkaline lakes, combined with current understanding of CaCO3 precipitation kinetics, indicates that the establishment of high alkalinity, high dissolved inorganic carbon (DIC), and CaCO3 supersaturation require compounds that inhibit or interfere with CaCO3 precipitation. Furthermore, the interplay between these factors may potentially affect fabric development in non-skeletal carbonates. In order to understand how these interlinked processes may have regulated PO4 concentrations and the processes and products of non-skeletal CaCO3 precipitation in the distant past, we conducted a detailed geological and geochemical study in two cores drilled in different portions of the Santos Basin, offshore southeastern Brazil, consisting of lacustrine carbonate rocks from the Lower Cretaceous Barra Velha Formation. We find that phosphorus in the sediments comes from two main products, phosphatic bioclasts and authigenic phosphate (of both primary and diagenetic origins). We also find that phosphorus occurs in concentrations of up to several thousand ppm in some intervals and is preferentially associated with some calcite textures potentially reflecting the primary sedimentary depositional conditions (e.g., upward-radiating aggregates of fibrous calcite, or “shrubs” and spherulitic aggregates of fibrous calcite, or “spherulites”). Microanalytical data from selected samples and high-Mg CaCO3 textures show median P values can be particularly high in crusts, shrubs and spherulitic calcite minerals interpreted here to have formed as primary to early diagenetic deposits, and roughly vary between 1000 and 2000 ppm (10.5–21.1 mmol/kg). The average P/(Ca + Mg) molar ratio values based on the same data for these three calcite textures are 1.45 ± 0.98, 1.13 ± 0.97 and 1.09 ± 0.90 mmol/mol, respectively, being as high as 4.80 mmol/mol in specific spots in “shrubby” textures. Although multiple source-to-sink mechanisms were likely involved in the P budget in lake waters and in the sediments, such as recycling and remobilisation of skeletal- and organic-bound phosphate, high alkalinity may have enhanced its accumulation in the lake’s waters. In light of current understanding of CaCO3 precipitation kinetics, we hypothesise that phosphate may have played a central role in maintaining high calcium carbonate saturation (14–45 < Ωcalcite ≤ 100–180). These conditions would have favoured growth of calcite crystals on pre-existing substrates over nucleation of finely particulate carbonate sediment. By combining these observations with theoretical geochemical considerations, we propose that phosphate inhibition of calcium carbonate precipitation was enhanced by high alkalinity, further sustaining CaCO3 supersaturation and favouring distinctive carbonate growth textures. This unique and relatively well-preserved example of non-skeletal carbonate production implies that similar regulation of CaCO3 precipitation kinetics and PO4 concentrations may have operated across other intervals of time in Earth’s history, both in non-marine and marine environments that pre-date the emergence of skeletal calcification.