We describe an improved method for purification of sedimentary vanadyl and nickel porphyrins (i.e., naturally occurring metalloalkylporphyrins). For the purpose of compound-specific isotopic analyses, various sedimentary porphyrins were purified from the complex natural mixtures by the dual-step high-performance liquid chromatography (HPLC) method. The high-sample-capacity reversed-phase HPLCs by adding N,N-dimethylformamide to the mobile phase allow an efficient collection of fractions containing the target compounds even using analytical-scale columns. Furthermore, this method achieved improved chromatographic resolutions but significantly reduced the overall retention time down to 60% compared with the previous work. The target compounds were then isolated with the normal-phase HPLC with the baseline-resolution, which is necessary to avoid chromatographic isotopic fractionation. One of the advantages of this method is that it requires neither derivatization nor demetallation. The purity of these isolated compounds was demonstrated by various HPLC online detection methods utilizing a photodiode-array detector, a mass selective detector. The overall recoveries of Ni porphyrin, VO porphyrin, and porphyrin-free base, respectively, were estimated to be approximately 50-60%, 65%, and 85%.