Processing and storage of apple juice often triggers quality deterioration regarding nutritional valuable compounds and unfavourable color changes resulting from browning. Fluorescence and near-infrared (NIR) spectroscopy were applied to detect such quality loss in apple juice. Juice samples were produced from Malus x domestica ’Pinova’, stored at 20 °C for 4 days or heated at 80 °C for 10 min and stored at the same conditions. The quality of apple juice was measured by standard parameters such as soluble solids content, pH, CIE L*, a*, and b* values. Juice fluorescence spectra were recorded with fluorescence excitation at 250, 266, 355, and 408 nm and emission at 280-899 nm resulting in an excitationemission- matrix (EEM) of 1240×4 for each sample. The NIR transmittance spectra were recorded in the wavelength range 900-1350 nm. The often used color b*-value for monitoring browning was correlated with the EEM variation and a reasonable calibration was built by means of n-way partial least squares (N-PLS) regression. The correlation coefficients were >0.9 in all treatments. NIR spectra were sensitive for predicting soluble solids content, but had poor capability to measure the color deterioration. Results indicated that the combination of NIR spectra and fluorescence EEM can be used to monitor the quality deterioration of apple juice.