A microscopic characterisation of the phase transitions associated with colossal magnetoresistance (CMR) in manganese perovskite oxides is a very important ingredient in the quest of understanding its underlying mechanism. Scanning tunneling microscopy (STM) is most suitable to investigate some of their reported hallmarks, including charge ordering, lattice distortions, and electronic phase separation. Here we investigate Bi1−xCaxMnO3 (BCMO) with x = 0.76. At this composition, BCMO develops an insulating charge-ordered phase upon cooling, whose study as a function of temperature will allow identifying atomic scale characteristics of the metal-insulator phase transition (MIT). We observe distinct atomic scale phases at temperatures above and below the MIT, with very different electronic and structural characteristics. Combining STM micrographs and current–voltage tunneling characteristics, we find that charge ordering correlates both with the local conduction state (metallic or insulating) and the local structural order. Furthermore, STM shows coexistence of these phases as expected for a first order phase transition.