The global demand for organic foods, driven by health benefits and consumer preferences, necessitates reliable methods for distinguishing organic products from their inorganic counterparts. This study investigates the application of dual handheld near infrared (NIR) spectroscopy devices, SCiO and Tellspec, combined with chemometric techniques for the nondestructive differentiation of organic and inorganic pineapple juices. The objective was to establish a rapid and robust method to differentiate organic pineapple juice from inorganic juice using unique spectral data from the two devices. Eighty-four pineapple juice samples were analyzed with preprocessing techniques, including mean centering, multiplicative scatter correction, standard normal variate, first derivative, and second derivative applied to the spectral data. Partial least squares discriminant analysis (PLS-DA) was employed for classification, and variable importance in projection (VIP) was used for optimal wavelength selection. The results demonstrated that the Tellspec scanner, particularly with second derivative preprocessing, achieved high accuracy in differentiating organic from inorganic pineapple juice. The fusion of data from both SCiO (740–1070 nm) and Tellspec (900–1700 nm) scanners, without preprocessing, coupled with the PLS-DA model, achieved perfect classification accuracy, sensitivity, and specificity (100 %) in both training and testing sets. This study highlights the potential of integrating dual handheld NIR spectroscopy with chemometrics to effectively and accurately classify organic and inorganic pineapple juices. The findings support using these advanced techniques for quality assurance and authentication in the food industry.