Understanding the authigenesis of carbonate fluorapatite through isotopic geochemistry can yield important information on fundamental geologic processes occurring on continental margins around the world. This is particularly true for phosphatic hardgrounds, which are often found in regions of upwelling, but of which questions remain about the initial formation and subsequent diagenesis. Here, we apply standard isotopes (δ13C, δ18O) alongside the novel clumped isotope (Δ47) used in this study for the first time to reconstruct the temperature of formation of carbonate ions within the lattice of sedimentary carbonate fluorapatite. We investigated phosphatic hardgrounds of Miocene age (12.7–10.8 Ma) sampled at El Capitan State Beach in the Monterey Formation. The range of isotopic signatures observed is between +1.5‰ and +8.0‰ for δ13C relative to the Vienna Peedee belemnite (VPDB) standard and −9.5‰ and −6.0‰ VPDB for δ18O, and values range between 0.599‰ and 0.615‰ for Δ47. The enriched δ13C and depleted δ18O signatures are suggestive of recrystallization within the methanogenic zone. Clumped isotope geochemistry further constrains this transformation as having taken place at a temperature of 61–66 °C ± 5 °C, in line with previous estimates for maximum burial of the Monterey Formation based on the silica phase transition. The calculated δ18O for the connate fluid shows an expected range for seawater composition for the Miocene, suggesting only minor contribution of silica-derived oxygen to the δ18O of carbonate fluorapatite. The combined conventional and clumped isotope data set also points out that methanogenesis took place deeper within the sediment in the middle Miocene than at present day within the Santa Barbara Basin. This study furthers our understanding of phosphogenesis and potential links to burial processes in the Monterey Formation, and it shows for the first time that the clumped isotope paleothermometer could be used to understand fundamental geochemical processes in authigenic sedimentary phosphates.