In this work, we have studied the substituent effect of several alkyl groups in the rate-determining step of the catalyzed Baeyer-Villiger (BV) reaction of phenyl alkyl ketones with performic (PFA) and trifluoroperacetic (TFPAA) acids, using quantum chemistry methods. Our results reveal that the substituent effect is more pronounced in the migration step barriers than in the corresponding addition step; that could change the rate-determining step (RDS) of the reaction, as observed in the oxidation of phenyl tert-butyl ketone with both peracids. In addition, the effect of the acid/peracid pairs used is also analyzed. We have demonstrated that the addition step is less susceptible to the acid/peracid nature since the acid strength and the nucleophilicity of the peracid have opposite effects. The effect of the acid/peracid pair is much more pronounced in the migration step because it only depends on the leaving ability of the acid, which in turn depends on its strength These observations are relevant for understanding the effects of the substrate, the peracid, and the catalyst on the switching of the RDS in the BV reaction.