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Stable carbon (C-13) and oxygen isotope (O-18) compositions of fossil brachiopod shells can be used to interpret paleoclimatic and paleoceanographic conditions. However, the initial isotopic composition of the living shells might be modified by diagenetic alteration. To assess the degree of this modification, we analyzed C-13 and O-18 and three common indicators of alteration in shells: minor element (manganese (Mn), iron (Fe), and strontium (Sr)) concentrations; cathodoluminescence (CL)/non-luminescence; and the shell microstructure of fossil Terebratalia coreanica and Laqueus rubellus (rhynchonellate brachiopod) shells from an exposure of conglomerates of the Tentokuji Formation (Pliocene, 3.85-2.75Ma) in northeastern Japan. Two indices were used to quantify the preservation state of shell microstructure: the altered fiber ratio (AFR) and the altered fiber and puncta-filling cement ratio (AF-PCR). We qualified the degree of luminescence by measuring the mean cathodoluminescence index (MCLI), defined as the mean R values in a particular area of a CL image with RGB colors. The C-13 and O-18 values were negatively correlated with AFR or AF-PCR and MCLI. The sampling spots with high Mn and Fe concentrations also exhibited relatively low C-13 and O-18. The C-13 and O-18 were more strongly correlated with Mn concentration than with Fe concentration. Therefore, of the three minor elements examined in this study, Mn concentration is the most reliable indicator of meteoric diagenesis in the studied shells. Unlike Mn and Fe concentrations, Sr concentrations in the modern and fossil brachiopod shells were similar, with overlapping ranges. This indicates that Sr concentration is not likely to be a good indicator of diagenetic alteration in the studied shells. Our study provides further evidence that multiple criteria should be applied and cross-checked when assessing diagenetic alteration of brachiopod shells.