Manganite perovskite oxides exhibit a wide range of properties relevant for catalysis, energy conversion and spintronics. Such behaviors can be deeply modified at the nanoscale where confinement and surface effects may prevail. Interesting properties could then emerge from manganite perovskite nanocrystals, although their synthesis remains a challenge. The present study reports a versatile synthesis of manganite perovskite nanocrystals by using molten salts as high temperature liquids in the 600–750 °C range. Through X‐ray diffraction, X‐ray photoelectron spectroscopy, scanning and transmission electron microscopies, we show that many substitutions on the A perovskite site are within reach by applying the approach to La2/3Sr1/3MnO3, La2/3Ca1/3MnO3 and La1/3Pr1/3Ca1/3MnO3 cubic‐shape nanocrystals with diameter of 20, 22 and 38 nm, respectively. The magnetic properties of these nanocrystals are then investigated at 5 K, highlighting the coexistence of a ferromagnetic phase typical of the bulk, with disordered and non‐magnetic domains, which presumably arise from the nanoscale and surface effects.