Voids and cracks can fatally degrade structural materials such as metals and ceramics but are tolerated in carbon fibre-reinforced plastic (CFRP) composites if monitored to prevent their growth to a critical size. Thus, the use of CFRPs as aeronautical structural materials requires an understanding of microscopic crack formation. However, this crack-formation mechanism remains unclear because experimental difficulties have hindered studies of relevant phenomena that occur before crack formation. Herein, we report high-resolution (~50 nm) and non-destructive three-dimensional observations of crack initiation and propagation under applied stress. This evaluation reveals that voids and cracks do not simply result from local stresses but instead occur largely through two competing nanoscale mechanisms, namely, fibre/plastic interface debonding and in-plastic crack initiation. Therefore, nanoscopic insights into these heterogeneities are essential for controlling crack initiation and determining reasonable safety margins for CFRP composite use.