Abstract In classification problems, isotonic regression has been commonly used to map the prediction scores to posterior class probabilities. However, isotonic regression may suffer from overfitting, and the learned mapping is often discontinuous. Besides, current efforts mainly focus on the calibration of a single classifier. As different classifiers have different strengths, a combination of them can lead to better performance. In this paper, we propose a novel probability calibration approach for such an ensemble of classifiers. We first construct isotonic constraints on the desired probabilities based on soft voting of the classifiers. Manifold information is also incorporated to combat overfitting and ensure function smoothness. Computationally, the extended isotonic regression model can be learned efficiently by a novel optimization algorithm based on the alternating direction method of multipliers (ADMM). Experiments on a number of real-world data sets demonstrate that the proposed approach consistently outperforms independent classifiers and other combinations of the classifiers’ probabilities in terms of the Brier score and AUC.