Nanoindentation is a most common experimental tool used for obtaining information on the mechanical behavior of materials. This is done by qualitatively relating the occurrence of pop‐ins (in the load–displacement plots) to microstructural changes such as dislocation formation, fracture of surface oxides, or slip transmission. The present study takes a first approach in directly verifying the micro‐plasticity processes that give rise to such pop‐ins by performing molecular dynamics indentation simulations in BCC Fe‐nanocrystals with a Σ5 symmetric tilt boundary. The simulations allow to track the material behavior throughout the indentation process, and illustrate that each pop‐in is related to twin formation, twin growth, de‐twinning, dislocation nucleation and glide, or dislocation–grain boundary interactions. For the particular Σ5 boundary considered, it is found that the pop‐ins are most closely associated with twin formation. Although pop‐ins have been related to dislocation nucleation, a direct correlation between twinning and pop‐ins has not been shown before. Adding C segregants to the Fe sample, reduced the formation of twins after initial yielding, and allowed for dislocation activity to become the more dominant deformation mechanism.