Nanoscale imprinting significantly increases the specific surface area and recognition capabilities of a molecularly imprinted polymer by improving accessibility to analytes, binding kinetics, and template removal. Herein, we present a novel synthetic route for a dual molecularly imprinted polymer (dual-MIP) of the carcinogen oxidative stress biomarkers 3-nitrotyrosine (3-NT) and 4-nitroquinolin-N-oxide (4-NQO) as coatings on graphene quantum-dot capped gold nanoparticles (GQDs-AuNPs). The dual-MIP was successfully coated on the GQDs-AuNPs core via a (3-mercaptopropyl) trimethoxysilane (MPTMS) linkage and copolymerization with the 3-aminopropyltriethoxysilane (APTMS) functional monomer. In addition, we fabricated a facile and compact three-dimensional electrochemical paper-based analytical device (3D-ePAD) for the simultaneous determination of the dual biomarkers using a GQDs-AuNPs@dual-MIP-modified graphene electrode (GQDs-AuNPs@dual-MIP/SPGE). The developed dual-MIP device provides greatly enhanced electrochemical signal amplification due to the improved electrode-specific surface area, electrocatalytic activity, and the inclusion of large numbers of dual-imprinted sites for 3-NT and 4-NQO detection. Quantitative analysis used square wave voltammetry, with an oxidation current appearing at -0.10 V for 4-NQO and +0.78 V for 3-NT. The dual-MIP sensor revealed excellent linear dynamic ranges of 0.01 to 500 μM for 3-NT and 0.005 to 250 μM for 4-NQO, with detection limits in nanomolar levels for both biomarkers. Furthermore, the dual-MIP sensor for the simultaneous determination of 3-NT and 4-NQO provides high accuracy and precision, with no evidence of interference from urine, serum, or whole blood samples.