Ex situ hot gas filtration (HGF) has been shown to be a simple and robust technique to upgrade the quality of flash pyrolysis oils. In this study, the secondary reactions inside the HGF unit and their impact on product yields and the chemical composition of bio-oils were investigated in a total of 18 experiments conducted at both pilot and bench reactor scales (1 and 0.1 kg/h), with beech wood (BW) and sunflower stalks (SFS). The impact of HGF on yields was found to be dependent on the extent of secondary reactions which, in turn, were determined by three parameters: (a) HGF temperature, (b) HGF char cake thickness, and (c) AAEM content of the raw feedstock. Nevertheless, independently of the conditions used, the drop in the organic yield was less than 10 wt % with both BW and SFS feedstocks. Our results demonstrated that (1) cracking reactions mainly took place in the homogeneous gas phase and (2) dehydration, coking, and decarboxylation reactions took place in the HGF char cake, probably catalyzed by the high AAEM content and the small size of the HGF char particles. Based on detailed chemical analysis of bio-oils, we propose several secondary reaction pathways to explain the interaction between the HGF char and the pyrolysis vapors, such as (1) ketonization of low Mw carboxyl functions via decarboxylation, (2) the formation of simple anhydro sugars by the selective cleavage of the glycosidic bond of the carbohydrate oligomers, and (3) the depolymerization of lignin oligomers. Further, our results suggest the interdependence of two factors which determine the impact of HGF: (a) the physical and chemical properties of HGF char and (b) the reactivity of the vapors.