The aim of this study was to compare the sporicidal effect of the disinfectants peracetic acid (PAA) or hydrogen peroxide (H2O2) applied as a fog or as a liquid. The efficacy of fogging of the disinfectants was tested in a closed isolator cabinet using highly heat and chemical-resistant spores of Geobacillus stearothermophilus. Fogging of a 0.06% solution of PAA resulted in over 5-log reduction of spores in 10 min, whereas for PAA used in liquid form the same reduction was achieved in 4.5 min. The inactivation curves for fog and liquid were fitted using three different models (Linear with shoulder, Weibull, Gauss-Eyring). This showed a shoulder for the fog with an estimated length of 4.1 min, but the D values, calculated for the linear parts of the curves, were not significantly different (1.1 and 0.8 min for the PAA fog and solution, respectively). Similar results were obtained for a 12% H2O2 solution, albeit that H2O2 was less effective compared to PAA, requiring 60 min to reach 3-log reduction when applied as a fog, with an estimated shoulder of 18.5 min. Fogging of a 0.06% peracetic acid solution effectively inactivated G. stearothermophilus spores. Overall, the data show that fogging can be an effective method of applying disinfectants but that a shoulder in the inactivation curves should be considered in process design. This study provides inactivation kinetics for disinfection using PAA or H2O2-based fog, which can aid in selection and validation of process parameters for disinfection of contained areas by fogging.