There is a growing need for portable, highly sensitive measuring equipment to analyze samples in-situ and in real time. For these reasons, it is becoming increasingly important to research for new experimental equipment to carry out this work with advanced, robust and low-cost devices. In this framework, a flexible, portable and low-cost fluorimeter (under 500€) based on a C12880MA MEMS micro-spectrometer with an Arduino compatible breakout board has been developed for trace analysis of biological substances. The proposed system can employ two selectable excitation sources for flexibility, one in the visible region at 405 nm (incorporated in the board) and an external LED at 365 nm in the UV region. This additional excitation source can be easily interchanged varying the LED type for other wavelengths of interest. The measurement process is micro-controlled, which allows a precise control of the spectrometer sensitivity by adjusting the integration time of each experiment separately. Data acquisition is easy, reliable and interfaced with a spreadsheet for fast spectra visualization and calculations. For testing the performance of the new device in fluorescence measurements, different fluorophore molecules which can be commonly found in biological samples, such as Fluorescein, Riboflavin, Quinine, Rhodamine b and Ru(II)-bipyridyl have been employed showing a high sensitivity in all cases and low quantitation limits (in the ppb range). It is also suitable for the study of other interesting phenomena, such as fluorescence quenching induced by chemical agents (such as halide anions or even auto-quenching). In this sense, an application for the chloride anions quantification in aqueous solutions, has been performed obtaining a LOD value of 18 ppm. Obtained results for all chemicals investigated with the proposed fluorimeter are always very similar in quantification figures or even better than literature data reported with commercial laboratory equipment