The BEST1 gene product bestrophin‐1, a Ca2+‐dependent anion channel, interacts with CaV1.3 Ca2+ channels in the retinal pigment epithelium (RPE). BEST1 mutations lead to Best vitelliform macular dystrophy. A common functional defect of these mutations is reduced trafficking of bestrophin‐1 into the plasma membrane. We hypothesized that this defect affects the interaction partner CaV1.3 channel affecting Ca2+ signaling and altered RPE function. Thus, we investigated the protein interaction between CaV1.3 channels and bestrophin‐1 by immunoprecipitation, CaV1.3 activity in the presence of mutant bestrophin‐1 and intracellular trafficking of the interaction partners in confluent RPE monolayers. We selected four BEST1 mutations, each representing one mutational hotspot of the disease: T6P, F80L, R218C, and F305S. Heterologously expressed L‐type channels and mutant bestrophin‐1 showed reduced interaction, reduced CaV1.3 channel activity, and changes in surface expression. Transfection of polarized RPE (porcine primary cells, iPSC‐RPE) that endogenously express CaV1.3 and wild‐type bestrophin‐1, with mutant bestrophin‐1 confirmed reduction of CaV1.3 surface expression. For the four selected BEST1 mutations, presence of mutant bestrophin‐1 led to reduced CaV1.3 activity by modulating pore‐function or decreasing surface expression. Reduced CaV1.3 activity might open new ways to understand symptoms of Best vitelliform macular dystrophy such as reduced electro‐oculogram, lipofuscin accumulation, and vision impairment.