The MIP-based electrochemical sensor designed for Lincomycin (LIN) was fabricated using an electropolymerization (EP) approach on a glassy carbon electrode (GCE) (3 mm) using 3-aminophenyl boronic acid (3-APBA) as a functional monomer. LIN is a biosynthetic drug obtained from the fermentation of streptomycin mutants and a common narrow-spectrum antibiotic with a strong antibacterial effect. The MIP-based electrochemical sensor's active surface area and porosity were increased using gold nanoparticles (AuNPs). The LIN/AuNPs/ANI@3-APBA/MIP/GCE sensor was evaluated electrochemically and morphologically using electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), and scanning electron microscopy (SEM). Furthermore, alterations on the electrode surface at the molecular and electronic levels were assessed using quantum chemistry calculations. The dynamic linear range of both designed sensors under optimized experimental conditions was 1.0 × 10-12-1.0 × 10-11 M for DPV and EIS methods. The impact of different interfering agents on the LIN peak current was examined to evaluate the selectivity of the study. In the presence of 1000-fold more interfering agents, RSD % and recovery % values (97.35-109.9 % for DPV and 98.08-108.56 % for EIS) were calculated. The proposed sensor's relative selectivity coefficient (k') was evaluated for both DPV and EIS methods, and it showed good selectivity for LIN in both methods compared to the NIP sensor. Moreover, the designed sensor was successfully applied to determine LIN in milk, apple juice, and orange juice samples. The created sensors were extremely sensitive, consistent, selective, and reproducible against the LIN molecule. Additionally, the Blue Applicability Grade Index (BAGI), Analytical Greenness Metric (AGREE), Analytical Greenness preparation (AGREEprep), and Analytical Greenness Assessment Tool for Molecularly Imprinted Polymers Synthesis (AGREEMIP) were also used to calculate the study's green profile score.