Copper phthalocyanine (CuPc) thin films have been deposited by a recently developed plasma-based method named glow-discharge-induced sublimation (GDS). The deposition of CuPc films has also been obtained by vacuum evaporation (VE) and the comparison of the two methods shows important structural differences. FT-IR and ion beam analyses (RBS-ERDA) show that the GDS-deposited films mainly consist of integer CuPc molecules, but at increasing deposition time the incorporation of damaged molecules becomes important. X-ray diffraction, FT-IR spectroscopy, and UV−vis analysis are used to study the microstructure of the CuPc films and point out that while the VE films consist of only α crystallites, a more disordered structure with the presence of both α and β polymorphs characterizes the GDS films. The latter films are also much more porous as shown by nitrogen physisorption measurements and SEM. Thermal treatments of the GDS films determine a decrease of the structural disorder at 250 °C and the complete transformation to the β polymorph at 290 °C.