Zooarcheological and geochemical evidence suggests Neanderthals were top predators, but their adherence to a strictly carnivorous diet has been questioned. Recent studies have demonstrated the potential of calcium stable isotopes to evaluate trophic and ecological relationships. Here, we measure the 44/42Ca values in bone samples from Mousterian contexts at Grotte du Bison (Marine Isotope Stage 3, Yonne, France) and Regourdou (Marine Isotope Stage 5, Dordogne, France) in two new Neanderthal individuals, associated fauna, and living local plants. We use a Bayesian mixing model to estimate the dietary composition of these Neanderthal individuals, plus a third one already analyzed. The results reveal three distinct diets: a diet including accidental or voluntary consumption of bone-based food, an intermediate diet, and a diet without consumption of bone-based food. This finding is the first demonstration of diverse subsistence strategies among Neanderthals and as such, reconciles archaeological and geochemical dietary evidence.