Phosphatic deposits from the Lower Cambrian Pedroche Formation (Sierra de Córdoba, Spain) provide key insights into early diagenetic mineralization processes during the Cambrian radiation. This study applies an integrated multi-analytical approach combining Raman spectroscopy, SEM–EDS, LA-ICP-MS, and ToF-SIMS to investigate mineralogical, elemental, and molecular signatures of phosphatized bioclastic carbonates and associated siliciclastic facies from the Los Lagares-1 borehole. Results reveal a systematic phosphatization gradient from carbonate-dominated skeletal rims to phosphate-rich interiors composed of carbonate fluorapatite with variable carbonate and hydroxyl substitution. Trace-element systematics and REE patterns indicate seawater-influenced phosphogenesis under suboxic porewater conditions, coupled to iron reduction and early diagenetic clay mineral formation. In contrast, the siliciclastic siltstone facies preserves poorly crystalline phosphate phases associated with detrital aluminosilicates and chlorite, reflecting distinct porewater chemistry and crystallization kinetics. ToF-SIMS mapping demonstrates spatial coupling between fluorine and phosphate within fossil structures, confirming fluorapatite formation and localized organic matter entombment. These results highlight the strong control of host lithology on phosphate crystallization pathways and trace-element redistribution, and provide new constraints on microbially mediated phosphogenesis in restricted Early Cambrian reef–lagoon systems along the northern Gondwanan margin.