Efficiently estimating properties of large and strongly coupled quantum systems is a central focus in many-body physics and quantum information theory. While quantum computers promise speedups for many of these tasks, near-term devices are prone to noise that will generally reduce the accuracy of such estimates. Here, we propose a sample-efficient and noise-resilient protocol for learning properties of quantum states building on the shadow estimation scheme [Huang et al., Nature Physics 16, 1050–1057 (2020)]. By introducing an experimentally friendly calibration procedure, our protocol can efficiently characterize and mitigate noises in the shadow estimation scheme, given only minimal assumptions on the experimental conditions. When the strength of noises can be bounded, our protocol approximately retains the same order of sample efficiency as the standard shadow estimation scheme, while also possessing a provable noise resilience. We give rigorous bounds on the sample complexity of our protocol and demonstrate its performance with several numerical experiments, including estimations of quantum fidelity, correlation functions and energy expectations, etc., which highlight a wide spectrum of potential applications of our protocol on near-term devices.