Food packaging faces the negative impact of synthetic materials on the environment, and edible coatings offer one alternative from filmogenic suspensions (FS). In this work, an active edible FS based on chitosan (C) and quinoa protein (QP) cross-linked with transglutaminase was produced. Thyme (T) and rosemary (R) essential oils (EOs) were incorporated as antimicrobial agents. Particle size, Z potential, and rheological parameters were evaluated. The antimicrobial activity against Micrococcus luteus (NCIB 8166) and Salmonella sp. (Lignieres 1900) was monitored using atomic force microscopy and image analysis. Results indicate that EOs incorporation into C:QP suspensions did not affect the Z potential, ranging from −46.69 ± 3.19 mV to −46.21 ± 3.83 mV. However, the polydispersity index increased from 0.51 ± 0.07 to 0.80 ± 0.04 in suspensions with EO. The minimum inhibitory concentration of active suspensions against Salmonella sp. was 0.5% (v/v) for thyme and 1% (v/v) for rosemary. Entropy and fractal dimension of the images were used to confirm the antimicrobial effect of EOs, which modified the surface roughness.