Thermodynamics of proton insertion across the perovskite-brownmillerite transition in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi mathvariant="normal">L</mml:mi> <mml:msub> <mml:mi mathvariant="normal">a</mml:mi> <mml

La$_{1-x}$Sr$_{x}$CoO3-$δ$ is a promising off-stoichiometric metal oxide that undergoes a topotactic perovskite ($δ$ = 0) to brownmillerite ($δ$ = 0.5) transition under electrochemical and thermochemical stimuli, with concomitant variations in its electrical, magnetic, thermal, and optical properties. Recent studies on thin-film cycling in electrochemical devices show incomplete reversibility of this transition, with significant acid-etching serving as a degradation mechanism. While earlier investigations examined the protonation of brownmillerite SrCoO2.5, the thermodynamics of protonation across the perovskite-to-brownmillerite transition remain poorly understood. In this work, we combine density functional theory calculations with predictions from universal machine-learning interatomic potentials to elucidate the energetics and implications of protonation across the transition for La0.5Sr0.5CoO3-$δ$. These calculations reveal negative hydrogen insertion energies and strong competition with oxygen vacancy formation across the transition for a wide range of conditions. The extent of protonation is primarily limited by the availability of Co 3d states to accommodate reduction by inserted hydrogen. Although hydrogen insertion is often thermodynamically favorable within a defect picture, a convex hull analysis of the resulting HyLa0.5Sr0.5CoO3-$δ$ phases reveals them to be unstable against decomposition into hydroxides among other products. This instability increases with hydrogen content and provides a thermodynamic basis for the acid-etching observed during electrochemical cycling. This work advances the fundamental understanding of protonation in La0.5Sr0.5CoO3-$δ$ and contextualizes experimental observations of related materials in the presence of moisture or H2.