Iron pyrite (FeS2) is an earth-abundant, non-toxic material that has a suitable band gap of 0.95 eV, a large optical absorption coefficient, and adequate carrier diffusion lengths for use in photovoltaic applications. However, its practical use is limited in part by poor understanding and control of doping. Here, we employ variable temperature Hall effect, electrical conductivity, optical transmission spectroscopy, and magnetization measurements supported by density functional theory (DFT) calculations to study, in detail, the impact of three transition metal impurities (cobalt, nickel, and chromium) on the properties of ultrapure pyrite single crystals grown in sodium polysulfide. By studying samples as a function of impurity concentration, we conclusively establish that cobalt is a nearly ideal donor in the dilute limit (<500 ppm Co) with a defect state that lies above the conduction band minimum, while nickel and chromium act as deep donors that barely affect the carrier concentration. Broad sub-band gap absorption features in the optical spectra of CoxFe1-xS2, NixFe1-xS2, and CrxFe1-xS2 samples are assigned using DFT models to specific electronic transitions between the impurity states and the pyrite bands. We also observe at low temperature several series of sharp absorption peaks in FeS2, NixFe1-xS2, and CrxFe1-xS2 that are likely caused by excitons and associated phonon replicas. Magnetization data are consistent with the other results and show that CoxFe1-xS2 magnetic behavior is similar to undoped samples at low Co concentration – indicating that cobalt donates one electron to the lattice to form nonmagnetic low-spin Co3+ – and develops a much larger paramagnetic response at higher Co concentrations owing to the increased Pauli paramagnetism from free carriers and paramagnetic behavior of occupied Co defect states (low-spin Co2+). NixFe1-xS2 acts as a well-behaved Curie paramagnet at all temperatures and concentrations explored with a charge state of Ni2+ deduced from the magnetic susceptibility, in agreement with DFT results. CrxFe1-xS2 also behaves as Curie paramagnets at all concentrations. While DFT calculations, in conjunction with electrical and optical data, indicate that Cr preferentially forms CrFe–VS pairs and should be in the low-spin Cr2+ state, susceptibility data shows Cr takes several electron configurations (low-spin Cr2+, high-spin Cr2+, and Cr3+) with some combination of each likely present in each sample. This discrepancy is not yet understood. By analyzing the results of each measurement (with exception of the Cr magnetic data), in conjunction with DFT calculations, we establish a self-consistent picture of the defect energy levels for each element. We determine that the CoFe defect state lies ~70 meV above the conduction band minimum, while NiFe and CrFe reside 378 and 209 meV below the conduction band, respectively. These results establish the basic doping behavior of three elements and provide a pathway for overcoming the key challenges to rational doping in pyrite.