Various food components, such as polyphenol and soluble dietary fiber, attenuate the decline of immunomodulatory function. We compared the bioactive components (isoflavone aglycone, total polyphenol, and low-molecular-weight soluble dietary fiber) in tempeh fermented with Rhizopus oligosporus (tempeh Rm), Rhizopus oryzae (tempeh Ro), or Rhizopus stolonifer (tempeh Rs). Tempeh Rs had the highest content for total isoflavone aglycone and low-molecular-weight soluble dietary fiber, which were 0.065 g and 2.5 g/100 g dry weight, respectively. Moreover, total polyphenol in tempeh Rs was 0.35 g/100 g dry weight, which was higher than that in unfermented soybean and tempeh Ro. We selected tempeh Rs and examined the therapeutic effects of dietary tempeh Rs on atopic dermatitis-like skin lesions induced by house dust mite in NC/Nga mice. The ingestion of tempeh Rs resulted in significant reductions in the skin severity scores for both ears and the immunoglobulin E concentration in experimental mice.