While Gaussian processes are a mainstay for various engineering and scientific applications, the uncertainty estimates don't satisfy frequentist guarantees, and can be miscalibrated in practice. State-of-the-art approaches for designing calibrated models rely on inflating the Gaussian process posterior variance, which yields confidence intervals that are potentially too coarse. To remedy this, we present a calibration approach that generates predictive quantiles using a computation inspired by the vanilla Gaussian process posterior variance, but using a different set of hyperparameters, chosen to satisfy an empirical calibration constraint. This results in a calibration approach that is considerably more flexible than existing approaches. Our approach is shown to yield a calibrated model under reasonable assumptions. Furthermore, it outperforms existing approaches not only when employed for calibrated regression, but also to inform the design of Bayesian optimization algorithms.