DNA-free genome editing using Cas9 ribonucleoprotein is advantageous because it introduces fewer potential undesirable genetic modifications than comparable methods. Here, we show a direct protein delivery system for plants using a cell-penetrating peptide-displayed polyion complex vesicle, CPP-PICsome, as a biological nanocarrier. With this system, we demonstrate nuclear genome editing by delivery of a Cas9 ribonucleoprotein complex in Arabidopsis thaliana callus.