We compared the biochemical profiles of Physalis ixocarpa hairy roots transformed with Agrobacterium rhizogenes ATCC and A4 strains with non-transformed root cultures. The studied clones of A4- and ATCC-induced hairy roots differed significantly; the latter showed greater growth potential and greater ability to produce secondary metabolites (tropane alkaloids) and to biotransform hydroquinone to arbutin. We compared glucose content, alanine and aspartate aminotransferase activity, and L-phenylalanine ammonia-lyase activity. We analyzed markers of prooxidant/antioxidant homeostasis: catalase, ascorbate peroxidase, oxidase, glutathione peroxidase and transferase activity, and the levels of ascorbate, glutathione, tocopherol and lipid peroxidation. We found that transformation induced strain-specific regulation, including regulation based on redox signals, determining the rate of allocation of carbon and nitrogen resources to secondary metabolism pathways. Our results provide evidence that A. rhizogenes strain-specific modification of primary metabolites contributed to regulation of secondary metabolism and could determine the ability of P. ixocarpa hairy root clones to produce tropane alkaloids and to convert exogenously applied hydroquinone to pharmaceutically valuable arbutin. Of the studied parameters, glucose content, L-phenylalanine ammonia-lyase activity and alanine aminotransferases activity may be indicators of the secondary metabolite-producing potential of different P. ixocarpa hairy root clones.