Increasing interest in nanoparticles of technological application has been improving their fabrication processes. The encapsulation of essential oils as bioactive compounds has proved to be an excellent alternative to the use of less environment friendly compounds. However, the difficulty of identifying their constitution and interaction with carrier agents have aroused scientific interest and a problem to overcome. Bilayer-based nanoparticles were developed using gelatin and poly-ε-caprolactone (PCL) aiming the encapsulation of Piper nigrum essential oil. based on atomic force microscopy images and dynamic light scattering analysis, the size of the unloaded and loaded nanoparticles was found around (194 ± 40) and (296 ± 54) nm, respectively. The spatial patterns revealed that the surface of nanoparticles presented different surface roughness, similar shapes and height distribution asymmetry, lower dominant spatial frequencies, and different spatial complexity. Traditional infrared spectroscopy allowed the identification of the nanoparticle outermost layer formed by the gelatin carrier, but microscopy-based infrared spectroscopy revealed a band at 1742 cm−1 related to the carbonyl stretching mode of PCL, as well as a band at 1557 cm−1 due to the amide II group from gelatin. The combination of microscopy and spectroscopy techniques proved to be an efficient alternative to quickly identify differences in chemical composition by evaluating different functional groups in bilayer PLC/gelatin nanoparticles of technological application.