Fermented juices have been suggested as vehicles for probiotic bacteria intake. However, low pH and presence of polyphenols, challenge the fermentation of plant matrices. The goals of this study were to determine the volatile compounds and amino acids profiles and hedonic characteristics of fermented apple juices (AJ), besides the impact of polyphenols and cell walls from apple parenchyma on Lactobacillus growth. Apple juices were inoculated with 7 log CFU/ml of single cultures of Lactobacillus acidophilus L10, L. casei L26, L. paracasei L33, L. plantarum 299v and L. rhamnosus LGG, and fermented for 48 h at 40°C. Volatile compounds were determined through headspace SPME/ GC-MS and flame ionization detector and free amino acids through HPLC-fluorescence detector, in triplicate. Overall assessment, odor, taste and visual appearance were appraised by untrained panelist (n = 29). AJs containing apple polyphenols (0–5 g/l), cell walls from apple parenchyma (0–1 g/l) and a mix of 0.5 g/l of polyphenols and 0.5 g/l of cell walls, were fermented. Profiles of volatile compounds of AJ fermented for 24 or 48 h were similar. Hexanal was consumed and diacetyl produced by all strains (P < 0.05). Acetoin production was the highest in juices fermented by LGG. Average scores of hedonic parameters corresponded to ‘like’ or ‘like moderately’. Amino acids profile in fermented juices was clearly dependent on the strain. Excepting L299v, all strains consumed methionine, phenylalanine, tryptophan, leucine and isoleucine. Glycine was produced by all strains and lysine by L10 and L33. L26, L33 and L299v were resistant to polyphenols up to 0.8 mg/ml of apple juice. Presence of cell walls was ineffective to improve lactobacilli growth but was protective against the effects of polyphenols for the strains L10 and L33. These observations point out the applicability of Lactobacillus strains for fermentation of AJ and indicate the strains the most resistant to polyphenols, which can be helpful to the fermentation of others fruit juices.