We report the development of a modified method for evaluating different reservoirs of sedimentary phosphorus (P) in ancient marine sedimentary rocks and in modern Fe-rich sediments. Utilising the existing SEDEX scheme for P partitioning in modern sediments, we initially demonstrate limitations in the application of the original scheme to sediments and rocks containing crystalline hematite and magnetite. We tested additional extractions for these crystalline Fe phases, using both synthetic minerals, and modern and ancient sediments. The addition of 6 h oxalate and 6 h citrate-dithionate-acetate extractions considerably enhanced the total recovery of synthetic magnetite and hematite to 88.7 ± 1.1% and 76.9 ± 3.8%, respectively. In addition, application of the 6 h oxalate extraction to synthetic P-containing magnetite recovered 93.9 ± 1.7% of the Fe present and 88.2 ± 12.8% of the co-precipitated P. Based upon these results we developed a modified SEDEX extraction scheme. The modified scheme was applied to modern Fe-rich sediments from Golfo Dulce, Costa Rica, which resulted in 16% higher Fe-bound P recovery. Application of the scheme to a variety of ancient marine rocks increased the recovery of Fe-bound P by up to 22%. We also highlight the potential for authigenic carbonate fluorapatite to convert to more crystalline apatite in ancient rocks during deep burial and metamorphism. We suggest that in such systems minimum and maximum estimates of the total reactive P pool may be calculated with and without the inclusion of crystalline P. It is noted that the application of the revised method may have important implications for understanding the cycling of P in ancient marine environments.