To obtain plasma polymerized (PP) layers with a high retention of the conjugated monomer structure, fragmentation during deposition should be minimized. Different methylated and halogenated thiophenes were used as monomers in plasma polymerization, and the influence of the substituent(s) on fragmentation during deposition was investigated. With the use of optical emission spectroscopy (OES) and mass spectroscopy (MS), it was found that methylated thiophenes show a low degree of fragmentation during deposition, whereas for halogenated thiophenes a high degree of fragmentation was observed. For a specific substituent, fragmentation was less for thiophene derivatives with substitution on the 2-position than on the 3-position. Disubstituted thiophenes always showed less fragmentation than their monosubstituted analogues. Due to the lower degree of fragmentation, PP layers from methylated thiophenes contained a higher amount of conjugated structures. Consequently, a higher conductivity was measured for these PP layers after iodine doping.