In the Philippines, chunks of calcium carbide are usually used as a ripening agent for mango samples, while chlorpyrifos is used to control pests and diseases in banana fruits. However, both of these agents can cause harm to human health. The acetylene gas from the calcium carbide produced during the ripening process of mango and the chlorpyrifos residue in the banana fruit can be inhaled and touched by humans. Likewise, considering the country’s economic standing, the development of low-cost and portable instruments is encouraged. To address these issues, a multi-spectral near-infrared light-emitting diode-based spectrometer was developed. This study aims to determine the calcium carbide residue and chlorpyrifos detection capability in mango and banana fruit, respectively, using the developed spectrometer prototype. The prototype is a spectrometer system that uses a graphical user interface, a DC power supply, and a black box. Fruit samples were scanned inside the black box and irradiated by the near-infrared lights from the circuit board. Partial least square regression and linear discriminant analysis showed 81.33% calcium carbide residue prediction capability and 88.9% correct classification, while it shows 74% chlorpyrifos residue prediction capability and 80% correct classification. Therefore, the multispectral near-infrared light-emitting diode-based spectrometer prototype has the chance to detect calcium carbide chemical residue in mango fruit and chlorpyrifos in banana fruit non-destructively.