Organic molecule conjugates usually arrange themselves into complex multiphase systems that are sensitive to processing and local chemical environment. Moreover, these conjugates are able to self-assemble at different scales, varying from nano- to macroscale. In addition, intermolecular interactions introduce structural variations in the molecular packing and large-scale ordering, which directly affects different physicochemical properties of the materials. Herein, we study the synthesis of polymer blends based on poly(ε)-caprolactone (PCL) with polyaniline (PANI) doped with the amino acid N-acetyl-l-cysteine (NAC). Samples were prepared either through solution casting or via electrospinning methods. The materials were characterized regarding their morphological, structural, and molecular properties at different length scales. From the results obtained, the relationship between changes in blend properties and different NAC concentrations was determined. Deep structural details have been unveiled by using different characterization techniques, including X-rays microcomputed tomography (Micro-CT), small- and wide-angle scattering (SAXS and WAXS), and differential scanning calorimetry (DSC). Our findings indicated that NAC enhances organization and crystallinity index of the blends and that a close relationship appears between the synthesis method and the internal micronanostructure. It is also shown that NAC modifies the molecular properties of PANI. Through spectroscopic techniques (UV–vis and resonant Raman), it was shown that NAC favors the formation of different forms of PANI. In addition, thermogravimetric analysis (TGA) and X-ray photoelectron spectroscopy (XPS) showed the formation of a supramolecular structure maintained by sulfur-π (SH-π) intermolecular interactions between PANI and NAC.