Tissue culture and mycorrhiza applications can provide disease-free seedlings and enhanced nutrient absorption, respectively, for organic farming. Ginger (Zingiber officinale Roscoe) is rich in phytochemicals and has various health-protective potentials. This study was aimed at determining effects of tissue culture and mycorrhiza applications alone or in combinations in organic farming on phytochemical contents (total phenolics and flavonoids [TP and TF, respectively], gingerol and shogaol homologues, phenolic acids, and carotenoids) and antioxidant capacities (DPPH [2,2-diphenyl-1-picrylhydrazyl] radical scavenging, oxygen radical absorbance (ORAC), and iron-chelating capacities [ICC]) in solvent-extractable (Free) and cell-wall-matrix-bound (Bound) fractions of ginger rhizome and Free fraction of the leaves in comparison with non-organics. Concentrations of the phytochemicals and antioxidant capacities, except for carotenoids and ICC, were significantly higher in organic ginger rhizomes and leaves than in non-organics regardless of the fractions and treatments (P < 0.05). Mycorrhiza application in organic farming significantly increased levels of TP, TF, gingerols, and ORAC in the Free fraction of the rhizome (P < 0.05). Furthermore, the combined application of tissue culture and mycorrhiza significantly increased concentrations of TF and gingerols and ORAC in the Free fraction of the rhizome (P < 0.05), suggesting their synergistic effects. Considerable amounts of phenolics were found in the Bound fractions of the rhizomes. Six-gingerol, ferulic acid, and lutein were predominant ones among gingerols, phenolic acids, and carotenoids, respectively, in ginger rhizomes. The results suggest that organic farming with mycorrhiza and tissue culture applications can increase concentrations of phytochemicals and antioxidant capacities in ginger rhizomes and leaves and therefore improve their health-protective potentials.