The mechanism responsible for deformation-induced crystalline-to-amorphous transition (CAT) in silicon is still under considerable debate, owing to the absence of direct experimental evidence. Here we have devised a novel core/shell configuration to impose confinement on the sample to circumvent early cracking during uniaxial compression of submicron-sized Si pillars. This has enabled large plastic deformation and in situ monitoring of the CAT process inside a transmission electron microscope. We demonstrate that diamond cubic Si transforms into amorphous silicon through slip-mediated generation and storage of stacking faults (SFs), without involving any intermediate crystalline phases. By employing density functional theory simulations, we find that energetically unfavorable single-layer SFs create very strong antibonding interactions, which trigger the subsequent structural rearrangements. Our findings thus resolve the interrelationship between plastic deformation and amorphization in silicon, and shed light on the mechanism underlying deformation-induced CAT in general. Sharper insights into stress-induced, crystalline-to-amorphous transitions in silicon can be realized with crack-resistant micropillars. Mechanical processes such as polishing during the manufacture of photovoltaic cell alter silicon's crystal structure and degrade device performance. Wei Zhang and Zhi-Wei Shan from Xi'an Jiaotong University in China and co-workers have now used high-resolution transmission electron microscopy to capture in situ images of these transitions in progress. The team designed a system of submicrometre pillars consisting of a crystalline silicon core encased in a nanoscale shell of amorphous silicon. The flexible shell helped prevent brittle fracture from occurring while the pillars were gradually compressed into mushroom shapes by an indentation tool. Real-time imaging revealed that mechanical force deformed the silicon framework through plastic motions only – a finding that upsets previous concepts of intermediate crystalline phases taking part in the amorphization process. A novel and effective crystalline-Si/amorphous-Si core/shell sample configuration has been devised. The malleable amorphous Si shell helped inhibit brittle fracture, provide the confinement to significantly raise the stress level, and extend the plastic flow in crystalline Si core. This enabled a real-time observation of the stress-induced crystalline-to-amorphous transition (CAT) process in Si. In situ TEM compression experiment demonstrated a direct amorphization process from the single crystalline diamond cubic Si phase, owing to the accumulation of plastic strain and profuse stacking faults. Deep insights of the CAT process have been achieved from density functional theory simulations.