The impact of the chemical structure and molecular order on the charge transport properties of two donor-acceptor copolymers in their neutral and doped states is investigated. Both polymers comprise 3,7-bis((E)-7-fluoro-1-(2-octyl-dodecyl)-2-oxoindolin-3-ylidene)-3,7-dihydrobenzo[1,2-b:4,5-b′] difuran-2,6-dione (FBDOPV) as electron-accepting unit, copolymerized with 9,9-dioctyl-fluorene (P(FBDOPV-F)) or with 3-dodecyl-2,2′-bithiophene (P(FBDOPV-2T-C 12 )). These copolymers possess an amorphous and semicrystalline nature, respectively, and exhibit remarkable electron mobilities of 0.065 and 0.25 cm 2 V -1 s -1 in field effect transistors. However, after chemical n-doping with 4-(1,3-dimethyl-2,3-dihydro-1H-benzoimidazol-2-yl)phenyl) dimethylamine (N-DMBI), electrical conductivities four orders of magnitude higher can be achieved for P(FBDOPV-2T-C 12 ) (σ = 0.042 S cm −1 ). More charge-transfer complexes are formed between P(FBDOPV-F) and N-DMBI, but the highly localized polaronic states poorly contribute to the charge transport. Doped P(FBDOPV-2T-C 12 ) exhibits a negative Seebeck coefficient of -265 µV K −1 and a thermoelectric power factor (PF) of 0.30 µW m −1 K −2 at 303 K which increases to 0.72 µW m −1 K −2 at 388 K. The in-plane thermal conductivity (κ || = 0.53 W m −1 K −1 ) on the same micrometer-thick solution-processed film is measured, resulting in a figure of merit (ZT) of 5.0 × 10 −4 at 388 K. The results provide important design guidelines to improve the doping efficiency and thermoelectric properties of n-type organic semiconductors.