Oxidation is the most commonly used method of passivating porous silicon (PSi) surfaces against unwanted reactions with guest molecules and temporal changes during storage or use. In the present study, several oxidation methods were compared in order to find optimal methods able to generate inert surfaces free of reactive hydrides but would cause minimal changes in the pore structure of PSi. The studied methods included thermal oxidations, liquid-phase oxidations, annealings, and their combinations. The surface-oxidized samples were studied by Fourier transform infrared spectroscopy, isothermal titration microcalorimetry, nitrogen sorption, ellipsometry, X-ray diffraction, electron paramagnetic resonance spectroscopy, and scanning electron microscopy imaging. Treatment at high temperature was found to have two advantages. First, it enables the generation of surfaces free of hydrides, which is not possible at low temperatures in a liquid or a gas phase. Second, it allows the silicon framework to partially accommodate a volume expansion because of oxidation, whereas at low temperature the volume expansion significantly consumes the free pore volume. The most promising methods were further optimized to minimize the negative effects on the pore structure. Simple thermal oxidation at 700 °C was found to be an effective oxidation method although it causes a large decrease in the pore volume. A novel combination of thermal oxidation, annealing, and liquid-phase oxidation was also effective and caused a smaller decrease in the pore volume with no significant change in the pore diameter but was more complicated to perform. Both methods produced surfaces that were not found to react with a model drug cinnarizine in isothermal titration microcalorimetry experiments. The study enables a reasonable choice of oxidation method for PSi applications.