Recent studies have shown the presence of an amorphous surface layer in nominally crystalline silicon nanocrystals (SiNCs) produced by some of the most common synthetic techniques. The amorphous surface layer can serve as a source of deep charge traps, which can dramatically affect the electronic and photophysical properties of SiNCs. We present results of a scanning tunneling microscopy/scanning tunneling spectroscopy (STM/STS) study of individual intragap states observed on the surfaces of hydrogen-passivated SiNCs deposited on the Au(111) surface. STS measurements show that intragap states can be formed reversibly when appropriate voltage–current pulses are applied to individual SiNCs. Analysis of STS spectra suggests that the observed intragap states are formed via self-trapping of charge carriers injected into SiNCs from the STM tip. Our results provide a direct visualization of the charge trap formation in individual SiNCs, a level of detail which until now had been achieved only in theoretical studies.