ABSTRACT Introduction Mutations in BEST1 gene have been linked to the development of refractory angle closure glaucoma (ACG). This study aims to delineate the clinical characteristics, genetic mutations, and disease progression in patients with autosomal recessive bestrophinopathy (ARB) and autosomal dominant Best vitelliform macular dystrophy (BVMD) who are presented with treatment-resistant ACG. Methods This retrospective analysis encompasses a comprehensive ophthalmic assessment, retinal imaging, and mutational profiling of six patients diagnosed with bestrophinopathy and concurrent ACG, with a particular emphasis on the risk of post-glaucoma filtration surgery malignant glaucoma (MG). Exome sequencing was conducted utilizing a next-generation sequencing (NGS) based gene panel. Results The cohort included five patients with ARB and one with BVMD, with a mean (±SD) age at ACG diagnosis of 35.1 ± 6.9 years. NGS analysis revealed homozygous BEST1 variants in four patients (ARB; cases 1–4) and a heterozygous BEST1 variant in one patient (BVMD; case 5). One patient (ARB; case 6), despite a recessive pedigree, showed a single heterozygous variant, suggesting the presence of an undetected heterozygous variant indicative of compound heterozygous autosomal recessive inheritance. A novel non-frameshift deletion (c.841_843delTTC; p.Phe281del) was identified in case 2. Surgical intervention was required due to uncontrolled glaucoma in all cases except case 4. All five cases that underwent glaucoma filtration surgery developed MG, which was effectively managed with combined iridozonulo-hyaloido-vitrectomy (IZHV) and pars plana vitrectomy (PPV). Cases 5 and 6, harboring a heterozygous pathogenic variant (c.241 G>A; p.Val81Met), experienced refractory MG and corneal decompensation necessitating multiple interventions. Conclusion Genomic analysis plays a pivotal role in the management of bestrophinopathies with ACG. Characterization of mutational types facilitates prognostication and enables timely interventions. IZHV with PPV emerges as a promising standalone or adjunctive procedure for the management of glaucoma among patients with BEST1 mutations and ACG.