This study focuses on the surface functionalization of citrate-stabilized gold nanoparticles (AuNPs) with disease-specific aptamers to enhance the detection of multifactorial disease (MD) biomarkers. MDs, characterized by complex pathophysiology involving multiple genetic and environmental factors, present significant diagnostic challenges. Aptamers, which are short, single-stranded oligonucleotides with high specificity and affinity for target molecules, have emerged as promising tools for biomarker detection. By utilizing response surface methodology (RSM) and face-centered central composite design (FCCCD), this research systematically optimized the bioconjugation process of AuNPs with different aptamer sequences, focusing on parameters such as AuNP size and aptamer concentration. The developed protocol in this study demonstrated that aptamer-functionalized AuNPs can be optimized for high yield, bioconjugation efficiency, stability, and surface coverage, making them suitable for diagnostic applications, particularly in surface-enhanced Raman spectroscopy (SERS). The findings provide a foundation for the development of customizable nanoprobes that can be adapted for the detection of various biomarkers associated with MDs, potentially improving early diagnosis and therapeutic outcomes.