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In this work, the indentation size effect and pop-in behavior are studied for indentations in undeformed and locally pre-deformed CaF2 single crystals, using both nanoindentation experiments and molecular dynamics simulations. To study the influence of dislocation density on the indentation behavior, small-scale indentations are carried out inside the plastic zone of larger indentations. This experiment is mimicked in the simulations by indenting a small sphere into the center of the residual impression of a larger sphere. The undeformed material shows the well-known pop-in behavior followed by the indentation size effect. Pre-deforming the material leads to a reduction in the indentation size effect both for experiments and simulations, which is in accordance with the Nix–Gao theory. Furthermore, the pop-in load is reduced in the experiments, whereas a smooth transition from elastic to plastic deformation is found in the simulations. There, plasticity is initiated by the movement of pre-existing dislocation loops in the vicinity of the plastic zone. The simulations thus give a detailed insight into the deformation mechanism during indentation and highlight the importance of the dislocation microstructure for the indentation size effect and dislocation nucleation.