The effects of minimal processing on the metabolite composition of orange juice were studied. Volatiles and nonvolatile polar compounds in Lane Late orange juices, with different pulp contents, treated by high-pressure homogenisation (HPH) at 150 MPa (at 58, 63 and 68 °C) and stored for 3 months at 3 °C were analysed by gas chromatography coupled to mass spectrometry (GC-MS) with automated data processing. A total of 92 volatiles and 22 polar components (trimethylsilyl, TMS, derivatives of sugars, organic acids and amino acids) were determined in fresh, processed and stored juices. Initially, concentration of fresh flavours (hydrocarbon terpenes and aldehydes) determined in the homogenised samples with the original pulp content was higher than that determined in fresh juice. During storage, desirable descriptors were better preserved in the juice processed at 68 °C with the lowest increase in off-flavours (alcohols and ketones). Generally, operations assayed did not exert a significant influence on polar metabolites, showing no effect on their decrease with time.