Limbal stem cell deficiency (LSCD) is a sight-threatening condition caused by the loss and/or dysfunction of limbal stem cells (LSCs), which are essential for corneal epithelial regeneration and homeostasis and are critical for maintaining corneal transparency. We have previously shown that specific inactivation of the endothelial mineralocorticoid receptor (MR) inhibits corneal neovascularization (CN) and that MR antagonists (MRA) improve corneal epithelial wound healing. This study investigated the therapeutic potential of MRA in LSCD and their mechanisms of action. Using a rat model of LSCD, systemic administration of spironolactone (SPL) or a more specific MRA, eplerenone, similarly reduced CN and corneal oedema, demonstrating MR-specific effects. SPL further limited inflammation, enhanced the corneal epithelial barrier, reduced corneal conjunctivalization and promoted nerve regeneration, highlighting its potential to improve corneal integrity. Transcriptomic analysis revealed that SPL upregulated genes associated with LSC maintenance (Tp63, Wnt6), corneal epithelial differentiation (Vdr, Fermt1, Ehf) and nerve regeneration (Sprr1a, Anxa1), while downregulating genes associated with angiogenesis (Kdr, Scube2), inflammation (Ccl2, Cxcl1) and fibrosis (Fbln1, Snai1). Conversely, transgenic rats overexpressing human NR3C2 encoding MR showed corneal epithelial irregularities and dysregulation of genes related to extracellular matrix remodeling and fibrosis (Matn3, Serpine2, Fmod, Bgn, Ddr2), angiogenesis (Nrp2, Scube1) and limbal cell function (Ifitm3). These findings demonstrate that activation of the MR pathway disrupts limbal and corneal homeostasis and that SPL effectively modulates critical mechanisms in LSCD, offering promising therapeutic potential to reduce CN and improve corneal epithelial barrier integrity.