Significant attempts are being made worldwide in an attempt to develop a tool that, with a simple analysis, is capable of distinguishing between different arboviruses. Herein, we employ molecular fluorescence spectroscopy as a sensitive and specific rapid tool, with simple methodology response, capable of identifying spectral variations between serum samples with or without the dengue or chikungunya viruses. Towards this, excitation emission matrices (EEM) of clinical samples from patients with dengue or chikungunya, in addition to uninfected controls, were separated into a training or test set and analysed using multi-way classification models such as n-PLSDA, PARAFAC-LDA and PARAFAC-QDA. Results were evaluated based on calculations of accuracy, sensitivity, specificity and F score; the most efficient model was identified to be PARAFAC-QDA, whereby 100% was obtained for all figures of merit. QDA was able to predict all samples in the test set based on the scores present in the factors selected by PARAFAC. The loadings obtained by PARAFAC can be used in future studies to prove the direct or indirect relationship of spectral changes caused by the presence of these viruses. This study demonstrates that molecular fluorescence spectroscopy has a greater capacity to detect spectral variations related to the presence of such viruses when compared to more conventional techniques.