Coronin-1A deficiency, caused by mutations in the CORO1A gene, is an autosomal recessive immunodeficiency characterized by T-cell dysfunction and is classified as severe combined immunodeficiency (SCID). This condition presents with lymphopenia, hypogammaglobulinemia, recurrent Epstein–Barr virus (EBV) infections, EBV-associated B-cell lymphoma and epidermodysplasia verruciformis. This case report presents a 32-year-old female with Coronin-1A deficiency, who developed IgM-dominant membranoproliferative glomerulonephritis (MPGN) alongside recurrent viral infections. This is the first reported case linking Coronin-1A deficiency with MPGN. The patient was treated with corticosteroids, which improved her renal function, but she succumbed to recurrent infections within a year. This case emphasizes the potential for renal disease in immunodeficient patients with persistent infections.