The present work reports on the investigation of oxidation states, local symmetry, and optical properties of manganese and iron species in natural cordierite (Mg, Fe)2Al4Si5O18, by means of energy-dispersive X-ray fluorescence, electron paramagnetic resonance (EPR), photoluminescence (PL) and optical absorption techniques. In particular, specific EPR characteristics show the presence of distinct Mn2+ octahedral sites in the crystal lattice, and a small amount of Mn4+ ions in tetrahedral sites. The absence of EPR signal ascribable to Mn4+ in octahedral sites turns out to be consistent with the lack of narrow PL lines from d3 ions in octahedral crystal field (CF). Evidence of Mn3+ in octahedral sites is instead found in steady-state and time-resolved PL measurements. EPR spectra give further details on iron site occupancy, showing the occurrence of Fe3+ ions in octahedral sites. Characteristics ascribable to all the identified metal species have been found in the optical absorption spectrum or in the PL excitation spectrum, as arising from the expected CF transitions of Fe2+, Fe3+, Mn2+, Mn3+, and Mn4+ ions. Interestingly, the results show a polarization-dependent correlation between the manganese luminescence and the pleochroic absorption band at about 17,000 cm−1. This result reveals a pleochroic contribution from the Mn3+ spin-allowed 5E→5T2 transition under the visible pleochroic band attributed to Fe2+(oct)→Fe3+(tet) transitions.