In this work we report nanostructuring of homoepitaxially grown {100} single crystal boron-doped diamond electrodes using 400 nm silica nanospheres template within MW PECVD process. This approach led to formation of hemispherical cavities with rough inner surfaces while preserving the sp³ carbon character of the material. Co-doping with Si atoms (concurrent with the boron doping) originated from plasma etching of silica was revealed. The nanostructuring led to significant (up to two orders of magnitude) increase of heterogeneous electron transfer rate constants within electrochemical measurements with surface-sensitive redox markers (ferro/ferricyanide, dopamine). Such enhancement can be caused by exposure of more reactive surfaces with other crystallographic orientations due to nanostructuring. These results reveal the potential of nanostructured BDD surfaces for creation of electrochemical sensors, spatially distributed surface modification, and entrapment of nanoparticles for development of composite electrodes.