This dataset contains LA-ICP-MS trace element concentrations from phosphatized bioclasts and associated mineral phases in a phosphoritic limestone interval at 101.8 m depth in the Los Lagares-1 borehole (Pedroche Formation, Córdoba, Spain). The data include major, minor, and trace elements, including rare earth elements (REE), measured in carbonate fluorapatite (CFA) and surrounding matrix. The dataset provides information on elemental distributions and geochemical variability linked to phosphogenesis and early diagenetic processes. These data contribute to the reconstruction of paleoenvironmental conditions and nutrient dynamics in a Lower Cambrian reef–lagoon system.