Specialty coffee with geographical indications (GI) labels has been regarded as one of the most expensive commercial coffee in Indonesia. In this research, we utilize a new approach to classify specialty coffee from Indonesia with different geographical origins using portable fluorescence spectroscopy. For samples, 80 coffee samples with 1 gram of each sample were provided: 40 samples of Gayo arabica coffee (origin: Gayo, Aceh), and 40 samples of Java Mocha robusta coffee (origin: Java). All coffee samples were subjected to the following sample preparation: roasting (at 200°C for 15 min), grinding, and sieving using mesh size 40 to obtain samples with a homogenous size of 420 micrometers. The extraction of coffee samples was done by using hot distilled water. After extraction and dilution, coffee samples were injected into the 10 mm standard cell. The fluorescence spectral acquisition was performed by using a GoyaLab fluorescence spectrometer. This spectrometer has four LED lamps with 365 nm peaks used as excitation sources. The principal component analysis (PCA) of preprocessed spectral data results showed that most coffee samples could be differentiated into two different clusters. The proposed method is easy, and affordable to be adopted by many coffee industries in Indonesia.