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Poly(o-methoxyaniline) emeraldine-salt form (ES-POMA) was chemically synthesized using hydrochloric acid and subjected to a heat treatment (HT) process for 1 h at 100 °C (TT100) and 200 °C (TT200). The HT process promoted a progressive decrease in crystallinity. The Le Bail method revealed a decomposition from tetrameric to trimeric-folded chains after the HT process. The unheated POMA-ES presented a globular vesicular morphology with varied micrometric sizes. The heat treatment promoted a reduction in these globular structures, increasing the non-crystalline phase. The boundary length (S) and connectivity/Euler feature (χ) parameters were calculated from the SEM images, revealing that ES-POMA presented a wide distribution of heights. The TT100 and TT200 presented a narrow boundary distribution, suggesting smoother surfaces with smaller height variations. The UV-VIS analysis revealed that the transition at 343 nm (nonlocal π → π*) was more intense in the TT200 due to the electronic delocalization, which resulted from the reduced polymer chain caused by the HT process. In addition to the loss of conjugation, counter ion withdrawal reduced the ion-chain interaction, decreasing the local electron density. This result shows the influence of the chlorine counter ions on the peaks position related to the HOMO → LUMO transition, since the π → polaron transition occurs due to the creation of the energy states due to the presence of counter ions. Finally, the electrical conductivity decreased after the HT process from 1.4 × 10−4 S.cm−1 to 2.4 × 10−6 S.cm−1 as result of the polymer deprotonation/degradation. Thus, this paper proposed a systematic evaluation of the POMA molecular structure and crystallite size and shape after heat treatment.