Packaged coconut water offers various options, from pure to those with added sugars and other additives. While the purity of coconut water is esteemed for its health benefits, its popularity also exposes it to potential adulteration and misrepresentation. To address this concern, our study combines Fourier transform infrared spectroscopy (FTIR) and machine learning techniques to detect potential adulterants in coconut water through classification models. The dataset comprises infrared spectra from coconut water samples spiked with 15 different types of potential sugar substitutes, including: sugars, artificial sweeteners, and sugar alcohols. The interaction of infrared light with molecular bonds generates unique molecular fingerprints, forming the basis of our analysis. Departing from previous research predominantly reliant on linear-based chemometrics for adulterant detection, our study explored linear, non-linear, and combined feature extraction models. By developing an interactive application utilizing principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE), non-targeted sugar adulterant detection was streamlined through enhanced visualization and pattern recognition. Targeted analysis using ensemble learning random forest (RF) and deep learning 1-dimensional convolutional neural network (1D CNN) achieved higher classification accuracies (95% and 96%, respectively) compared to sparse partial least squares discriminant analysis (sPLS-DA) at 77% and support vector machine (SVM) at 88% on the same dataset. The CNN’s demonstrated classification accuracy is complemented by exceptional efficiency through its ability to train and test on raw data.