Potential applications of the earth-abundant, low-cost, and non-critical perovskite CaTi1–x Fe x O3−δ in electrocatalysis, photocatalysis, and oxygen-transport membranes have motivated research to tune its chemical composition and morphology. However, investigations on the decomposition mechanism(s) of CaTi1–x Fe x O3−δ under thermochemically reducing conditions are limited, and direct evidence of the nano- and atomic-level decomposition process is not available in the literature. In this work, the phase evolution of CaTi1–x Fe x O3−δ (x = 0–0.4) was investigated in a H2-containing atmosphere after heat treatments up to 600 °C. The results show that CaTi1–x Fe x O3−δ maintained a stable perovskite phase at low Fe contents while exhibiting a phase decomposition to Fe/Fe oxide nanoparticles as the Fe content increases. In CaTi0.7Fe0.3O3−δ and CaTi0.6Fe0.4O3−δ, the phase evolution to Fe/Fe oxide was greatly influenced by the temperature: Only temperatures of 300 °C and greater facilitated phase evolution. Fully coherent Fe-rich and Fe-depleted perovskite nanodomains were observed directly by atomic-resolution scanning transmission electron microscopy. Prior evidence for such nanodomain formation was not found, and it is thought to result from a near-surface Kirkendall-like phenomenon caused by Fe migration in the absence of Ca and Ti co-migration. Density functional theory simulations of Fe-doped bulk models reveal that Fe in an octahedral interstitial site is energetically more favorable than in a tetrahedral site. In addition to coherent nanodomains, agglomerated Fe/Fe oxide nanoparticles formed on the ceramic surface during decomposition, which altered the electrical transport mechanism. From temperature-dependent electrical conductivity measurements, it was found that heat treatment and phase decomposition change the transport mechanism from thermally activated p-type electronic conductivity through the perovskite to electronic conduction through the iron oxide formed by thermochemical decomposition. This understanding will be useful to those who are developing or employing this and similar earth-abundant functional perovskites for use under reducing conditions, at elevated temperatures, and when designing materials syntheses and processes.