Doping of polymer semiconductors such as poly(2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT) with acceptor molecules such as 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) is widely used to tune the charge transport and thermoelectric (TE) properties in thin films. However, the mechanism of dopant insertion in the polymer matrix, insertion kinetics, and the ultimate doping levels reached have been investigated only marginally. This contribution addresses the effect of alkyl side chain length on the doping mechanism of a series of PBTTTs with linear side chains ranging from n-octyl to n-octyldecyl. The study focuses on thin films oriented by high-temperature rubbing and sequentially doped in F4TCNQ solution. Structure–property correlations are established as a function of side chain length by a combination of transmission electron microscopy, polarized UV–vis–NIR spectroscopy, and charge transport/thermopower measurements. Intercalation of F4TCNQ into the layers of side chains results in the expansion of the lattice along the side chains and the contraction along the π-stacking direction for all polymers. The extent of lattice expansion decreases with the increasing side chain length. UV–vis–NIR spectroscopy demonstrates integer charge transfer for all investigated PBTTTs. The doping kinetics and the final doping level depend on both the side chain length and packing. Highly disordered n-octyl and crystalline n-octyldecyl side chain layers tend to hamper dopant diffusion in the side chain layers contrary to n-dodecyl side chains that can host the highest proportion of dopants. Consequently, the best TE properties are observed for C12-PBTTT films. Alignment of the polymers significantly enhances the TE performance by increasing the charge conductivity and the thermopower along the rubbing direction. Aligned films of C12-PBTTT show charge conductivities of 193 S cm–1 along the rubbing direction and power factors of approximately 100 μW m–1 K–2 versus a few μW m–1 K–2 for nonoriented films.