Hydrophobicity has limited the efficiency of many drugs. To improve this, gold–silver alloy nanocomposites covered with carbon-based quantum dots were synthesized as a platform to reduce the drugs’ hydrophobicity. Using the hydrophobic drug Andrographolide as a model, it was demonstrated that these nanocomposites can decrease Andrographolide’s hydrophobicity (Log P from 2.632 to 0.56) without encapsulating the drug. Entry within prostate cancer (PC-3) cells and in vitro localization of the nanocomposites and Andrographolide was observed qualitatively via confocal microscopy and their identity confirmed by SERS inside the PC-3 cells. MTS assays demonstrated the carbon-based quantum dot layer covering the metal core of the nanocomposites stabilizes the oxidation rate of the nanocomposite’s core metals. This was observed by a decrease in cytotoxicity in PC-3 cells when compared to other gold or silver nanosystems for similar timeframes published in the literature.