Milk has long been a vital nutrient source, but adulteration compromises its quality and introduces harmful substances, posing serious health risks to consumers. This study presents a rapid, and portable method for detecting milk adulterants, such as melamine, dicyanamide (DCD), and ammonium sulfate (AmS), at ultra-trace levels using surface-enhanced Raman spectroscopy (SERS). In this study, we systematically explored two often utilized forms of SERS substrates composed of silver nanoparticles (Ag NPs) of spherical shape—one with colloidal Ag NPs solutions, and another with thin film-based Ag NPs based SERS substrate. A comprehensive analysis showed that colloidal solution-based spherical-shaped Ag NPs provided higher signal intensity than Ag NP films when using R6G as a probe molecule. This difference is due to 3D adhesion and closer contact between the analyte and Ag NPs in the colloidal solution, compared to the Ag NP-based SERS films. This study combines SERS with machine learning (ML) to detect and quantify milk adulteration. SERS spectra, obtained using spherical Ag NPs, were analysed using ML models to classify various adulterants efficiently. The detection limits (LOD) for these adulterants were as low as 0.012 ppm, 0.02 ppm, and 0.13 ppm, respectively, with accuracies of 96%, 98%, and 97%. The optimized SERS substrate, which is cost-effective, enables the detection of low-concentration milk adulteration without the need for sample pretreatment. This method offers a simple approach and shows that the spherical Ag NPs remain stable over time, supporting their extended shelf life for practical food safety use. The key novelty of this work lies in the integration of a scalable, low-cost colloidal SERS substrate with machine learning-based quantification, delivering a rapid and reliable solution for real-time detection of milk adulteration in complex matrices without the need for elaborate sample preparation.