A critical approach to plasma sterilization is presented with the aim of sterilizing biocompatible materials such as TiO₂ and polymer implants. Oxygen plasma was applied to sterilize glass and aluminium samples containing Bacillus subtilis spores. Sterilization was performed with a low pressure weakly ionized oxygen plasma created with a RF generator with an output power of 300 W and frequency 27.12 MHz. The density of charged particles, density of neutral oxygen atoms and the electron temperature were about 1 × 10¹⁶ m⁻³, 1.5 × 10²² m⁻³ and 5 eV, respectively. The sterilization effects were observed by SEM and by bacterial cultivation. It was found that the surface recombination of O-atoms plays an important role, since it causes temperature changes in the substrate. The sterilization efficiency increased with increasing plasma exposure time. The results showed that the sterilization efficiency is not necessarily just the effect of oxygen plasma radical interactions, but also of the sample heating due to radical interaction with the substrate. Plasma sterilization should be done differently according to the substrate material used for sterilization.