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Abstract When an electron is removed from a conjugated polymer, such as poly(3‐hexylthiophene‐2,5‐diyl) (P3HT), the remaining hole and associated change in the polymer backbone structure from aromatic to quinoidal are referred to as a polaron. Bipolarons are created by removing the unpaired electron from an already‐oxidized polymer segment. In electrochemically‐doped P3HT films, polarons, and bipolarons are readily observed, but in chemically‐doped P3HT films, bipolarons rarely form. This is explained by studying the effects of counterion position on the formation of polarons, strongly coupled polarons, and bipolarons using both spectroscopic and X‐ray diffraction experiments and time‐dependent density functional theory calculations. The counterion positions control whether two polarons spin‐pair to form a bipolaron or whether they strongly couple without spin‐pairing are found. When two counterions lie close to the same polymer segment, bipolarons can form, with an absorption spectrum that is blueshifted from that of a single polaron. Otherwise, polarons at high concentrations do not spin‐pair, but insteadJ‐couple, leading to a redshifted absorption spectrum. The counterion location needed for bipolaron formation is accompanied by a loss of polymer crystallinity. These results explain the observed formation order of single polarons, coupled single polarons, and singlet bipolarons in electrochemically‐ and chemically‐doped conjugated polymers.