Clostridium pasteurianum is a promising producer of the bulk chemicals 1,3‐propanediol and n‐butanol (BuOH), with significantly different product patterns and physiology from other typical Clostridia. Nevertheless, its growth and product formation are ultimately limited by the accumulation of inhibiting products, especially by BuOH. In this study, we implemented in situ gas stripping for BuOH removal and compared the stripping performance of external nitrogen (N2) and fermentation effluent gas (FG) from the process itself. Gas stripping was studied in fermentations of glycerol and a mixture of glycerol and glucose. In general, N2 exhibits favourable physical properties to strip out BuOH from an aqueous phase. However, in situ removal of butanol in C. pasteurianum culture with N2 stripping strongly perturbs the culture conditions such as the redox potential and thus the physiology of the microorganism, leading to enhanced formation of organic acids, especially in cosubstrate fermentation, whereas the use of FG does not show such perturbations. In an effort to explore the use of FG for gas stripping the effects of FG circulation rate and stirring speed of the bioreactor on BuOH stripping efficiency and the fermentation performance were studied in more detail. Mass transfer coefficient (kSa) of BuOH in the bioreactor was also characterized at different gas circulation rates and stirring speeds. In a fermentation of glycerol with FG stripping at a relatively high gas flow rate (7 vvm) as high as 39.2 g/L BuOH (total) and 53.7 g/L 1,3‐PDO can be simultaneously produced. The results are discussed in view of further process optimization and scale up.