Rationale A key element of studies that utilise ion mobility mass spectrometry (IM‐MS) under native electrospray conditions for the analysis of protein–ligand binding is the maintenance of the native conformation of a protein during the removal of bulk solvent. Ruotolo and co‐workers have demonstrated that the binding and subsequent dissociation of the anionic component of inorganic salts stabilise native protein conformations in the gas phase. In this study, we investigated the effect that organic acid fragments identified from a fragment‐based drug discovery (FBDD) campaign might have on the gas‐phase stability of carbonic anhydrase II (CA II). Methods We utilised native IM‐MS to monitor changes in the conformation of CA II in the absence and presence of four acidic fragments. By performing a series of collision‐induced unfolding (CIU) experiments we determined the effect of fragment binding on the gas‐phase stability of CA II. Results Binding and dissociation of acidic fragments result in increased gas‐phase stability of CA II. CFU experiments revealed that the native‐like compact gas‐phase conformation of the protein is stable with higher degree of pre‐activation when bound to a series of acidic fragments. Importantly, although acetate was present in high concentrations, the stabilising effect was not observed without the addition of the acidic fragments. Conclusions Binding and subsequent dissociation of acidic fragments from CA II significantly delayed CIU in a manner which is probably analogous to the effect of inorganic anions. Furthermore, we saw a slightly altered stabilising effect between the different fragments investigated in this study. This suggests that the prevention of CIU by organic acids may be tuneable to specific properties of a bound ligand. These observations may open avenues to exploit IM‐MS as a screening platform in FBDD.