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Incorporation of polar side chains on organic semiconducting materials have been used recently in thermoelectric materials to increase dopant:semiconductor miscibility and stability to further increase the performance and durability of devices. However, investigations into how polar side chains can affect the structure and energetics of polythiophenes compared to non-polar alkyl side chains are usually carried out using materials with no common morphological structure. Within this work we systematically investigate the increase in polar side chain content on poly(3-hexylthiophene) (P3HT) and how the optical, electrochemical, and structural properties are affected. We find a decreasing degree of aggregation with increasing polar side chain content leading to lower charge carrier mobilities. Upon doping with 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ), we find that the electrical conductivity is reduced when incorporating the polar side chain and no stabilising effect is demonstrated when annealing the doped thin films at raised temperatures. This study emphasises that polar functionalities do not always increase dopant:semiconductor interactions and can harm desirable structural and electrical characteristics, and therefore should be incorporated into organic semiconductors with caution.