Molecular doping of conjugated polymers (CPs) plays a vital role in optimizing organic electronic and energy applications. For the case of organic thermoelectrics, it is commonly believed that doping CPs with a strong dopant could result in higher conductivity (σ) and thus better power factor (PF). Herein, by investigating thermoelectric performance of a polar side‐chain bearing CP, poly(3‐(methoxyethoxyethoxy)thiophene) (P3MEET), vapor doped with fluorinated‐derivative of tetracyanoquinodimethane FnTCNQ (n = 1, 2, 4), we show that using strong dopants can in fact have detrimental effects on the thermoelectric performance of CPs. Despite possessing higher electron affinity, doping P3MEET with F4TCNQ only results in a σ (27.0 S/cm) comparable to samples doped with other two weaker dopants F2TCNQ and F1TCNQ (26.4 and 20.1 S/cm). Interestingly, F4TCNQ‐doped samples display a marked reduction in the Seebeck coefficient (α) compared to F1TCNQ‐ and F2TCNQ‐doped samples from 42 to 13 μV/K, leading to an undesirable suppression of the PF. Structural characterizations coupled with Kang‐Snyder modeling of the α–σ relation show that the reduction of α in F4TCNQ‐doped P3MEET samples originates from the generation of low mobility carrier within P3MEET's amorphous domain. Our results demonstrate that factors such as dopant distribution and doping efficiency within the crystalline and amorphous domains of CPs should play a crucial role in advancing rational design for organic thermoelectrics.