In the mining of perlite deposits, controlling the generation of fine particles and the concentration of metals is of outstanding importance to meet the environmental and market requirements. Particle size and chemical purity are conventionally manipulated during the processing of the ore to achieve high product specifications. However, the current practices do not consider a proactive approach that focuses in the in-pit characterisation of the ore that would minimise the environmental impact and optimise the mining process since its early stages. This paper presents a method for the in-pit detection of the perlite ore variability that is related to the generation of fine particles and the elevated concentration of metals. Particle size and chemical purity showed to be dependent on the mineralogical variations of the ore, specifically opal and montmorillonite. Using a portable infrared spectrometer, an index that establishes the relative proportions of these minerals in the perlite ore was created. Such index provided insight into the correlation between mineralogy, fine particles and concentration of metals. Consequently, the index could be used not only for mineralogical determination but also as a predictor of the presence of the main impurities in the perlite ore. These results can be implemented in perlite mining to reduce the generation of waste and can influence the production of high-quality perlite products.