This work aimed to determine the effect of homogenization pressures (HPH) and addition of trehalose on the functional and technological properties of low pulp mandarin juice (LPJ). A set of experiments was designed, combining a non-targeted metabolomic H-1 NMR based approach together with suspended pulp and transmittance, hesperidin, vitamin C and antioxidant activity analysis. Suspended pulp increased with HPH and trehalose addition. Flavonoid hesperidin initially decreased with HPH but trehalose addition resulted in less flavonoid degradation during storage, increasing the effect with the HPH. Vitamin C was not affected by trehalose and pressure treatment but more Vitamin C degradation was observed in trehalose samples during storage. Antiradical activity improvement by trehalose was conditioned by homogenization pressures and specific bioactive compounds. H-1 NMR based approach highlighted the HPH effect on the microbiological aspects of low pulp mandarin juice by the identification of key molecules responsible of the microorganism profile evolution during storage. (C) 2016 Elsevier Ltd. All rights reserved.