Cloud microphysics is a critical aspect of the Earth’s climate system, which involves processes at the nano- and micrometer scales of droplets and ice particles. In climate modeling, cloud microphysics is commonly represented by bulk models, which contain simplified process rates that require calibration. This study presents a framework for calibrating warm-rain bulk schemes using high-fidelity super-droplet simulations that provide a more accurate and physically based representation of cloud and precipitation processes. The calibration framework employs ensemble Kalman methods including ensemble Kalman inversion (EKI) and unscented Kalman inversion (UKI) to calibrate bulk microphysics schemes with probabilistic super-droplet simulations. We demonstrate the framework’s effectiveness by calibrating a single-moment bulk scheme, resulting in a reduction of data-model mismatch by more than $75\%$ compared to the model with initial parameters. Thus, this study demonstrates a powerful tool for enhancing the accuracy of bulk microphysics schemes in atmospheric models and improving climate modeling.