The process of formation of silicon nanobonds between opposing silicon tips was observed in situ with a transmission electron microscope at room temperature. Silicon nanobonding was formed by soft contact of the tips driven by MEMS actuators. According to the observations of the nanobond formation at atomic resolution, the structure of the bond evolved in three stages: (1) the formation of an initial amorphous bond, (2) its transformation into a mixture of amorphous silicon and nano-sized crystalline grains and (3) the transformation of a multi-crystalline bond.