•NIRS was applied to predict total anthocyanins content (TAC) and total phenolic compounds (TPC) in wax jambu fruit.•The PLS analysis for quantitative prediction of both parameters gave excellent accuracy values.•For TAC, PLS model produced prediction accuracy (rp=0.98, RMSECV=7.56mgL−1, RMSEP=9.0mgL−1 and RPD=5.19).•For TPC, PLS model produced prediction accuracy (rp=0.94, RMSECV=19.01mgL−1, RMSEP=22.18mgL−1 and RPD=3.27). The aim of this work was to develop an analytical method to predict total anthocyanins content (TAC) and total phenolic compounds (TPC) in intact wax jambu fruit Syzygium malaccense (L.) Merryl et Perry using near-infrared spectroscopy (NIRS) and partial least squares (PLS). The estimation accuracy was based on parameters such as root mean square error of prediction (RMSEP), correlation coefficients calibration (rc) and prediction (rp) set and ratio of performance to deviation (RPD). TAC, rp=0.98, RMSEP=9.0mgL−1 and RPD=5.19 were attained using second derivative pre-treatment. TPC, rp=0.94, RMSEP=22.18 (mg gallic acid equivalents (GAE)/100g) and RPD=3.27 (excellent accuracy) were also obtained using second derivative pre-treatment. These findings suggest that the NIRS and PLS algorithms can be used to determine TCA and TPC in intact wax jambu fruit.