The use of protonated water clusters and protonated ethanol clusters as reagent ions has been evaluated for the resolution of an interference encountered in CIMS when measuring monoterpenes (C10H16) and linalool (C10H18O) simultaneously. To this end, the reactions of H3O+·(H2O)n (n = 1–3), (C2H5OH)mH+ (m = 1–3) and (C2H5OH·H2O)H+ with α-pinene and linalool have been characterized in a flowing afterglow-selected ion flow tube (FA-SIFT) instrument at a SIFT He buffer gas pressure of 1.43 hPa and a temperature of 298 K. All reactions with linalool were found to occur at the collision limit. The reaction of (C2H5OH)2H+ with α-pinene proceeds at half the collision rate and both the reactions of (C2H5OH)3H+ and H3O+·(H2O)3 with α-pinene have a very low rate constant. All other reactions involving α-pinene proceed at the collision rate. The reactions of H3O+·H2O, H3O+·(H2O)2, C2H5OH2+, (C2H5OH·H2O)H+ and (C2H5OH)2H+ with α-pinene mainly proceed by proton transfer. Additionally, ligand switching channels have been observed for the reactions of (C2H5OH)2H+ and H3O+·(H2O)2 with α-pinene. Protonated linalool was observed as a minor product for the reactions of (C2H5OH·H2O)H+ and H3O+·(H2O)n (n = 1–3) with linalool. For all linalool reactions, a contribution of the dissociative proton transfer product at m/z 137 was found and this ion was the main product ion for the reactions with H3O+·H2O, C2H5OH2+ and (C2H5OH·H2O)H+. For the (C2H5OH·H2O)H+/linalool reaction, ligand switching with both water and ethanol has been observed. Major ligand switching channels were observed for the reactions of (C2H5OH)2H+, (C2H5OH)3H+ and H3O+·(H2O)2 with linalool. Also, for the H3O+·(H2O)3/linalool reaction, several ligand switching channels have been observed. These results are discussed in view of their applicability for the selective detection of monoterpenes and linalool with CIMS instrumentation such as SIFT-MS, PTR-MS and APCI-MS.