Natural polyphenolic compounds play a pivotal role in biological processes and exhibit notable antioxidant activity. Among these compounds, chlorogenic acid stands out as one of the most widespread and important polyphenols. The accurate detection of chlorogenic acid is crucial for ensuring the quality and classification of the raw materials used in its extraction, as well as the final products in the food, pharmaceutical, and cosmetics industries that contain this bioactive compound. Raman spectroscopy emerges as a powerful analytical tool, particularly in field applications, due to its versatility and sensitivity, offering both qualitative and quantitative analyses. By using the self-assembly of gold nanoparticles at liquid–liquid interfaces and the developed “aqua-print” process, we propose a facile and inexpensive route to fabricate enhanced substrates for surface-enhanced Raman spectroscopy with high reproducibility. To ensure substrate reliability and accurate molecule detection in SERS experiments, a benchmarking procedure was developed. This process involved the use of non-resonant rhodamine 6G dye in the absence of charge transfer and was applied to all synthesized nanoparticles and fabricated substrates. The latter revealed the highest enhancement factor of 4 × 104 for 72 nm gold nanoparticles among nanoparticle diameters ranging from 14 to 99 nm. Furthermore, the enhanced substrate was implemented in the detection of chlorogenic acid with a concentration range from 10 μM to 350 μM, demonstrating high accuracy (R2 > 99%). Raman mapping was employed to validate the good uniformity of the signal (the standard deviation was below 15%). The findings of this study were also supported by DFT calculations of the theoretical Raman spectra, demonstrating the formation of the chlorogenic acid dimer. The proposed method is strategically important for the development of the class of in-field methods to detect polyphenolic compounds in raw materials such as plants, extracted plant proteins, and polyphenolic compounds.