Organic materials, such as chitin incubated solution (CIS) combined with neem oil (NO), nano silver silica (NSS), and Bordeaux mixture (BDM), were applied with and without agricultural chemicals (AC) (insecticide and fungicide) to investigate scab and mealybug occurrences and fruit qualities on ‘Niitaka’ pear trees in orchards in 2006. Fruits and leaves grown under CIS+NO without AC had less than 30%, scab occurrence, but CIS+NSS or CIS+BDM without AC had higher scab occurrence. Organic materials with AC decreased the scab to less than 20%. All treatments decreased mealybug occurrences to less than 10%, except for the fruits grown under CIS+BDM without AC. Fruit qualities varied among the treatments. Hunter value a, representing for the redness degree, was higher for fruits treated with CIS+NSS and CIS+BDM without AC than those with AC. Fruits treated with organic materials without AC had greater total phenolic and flavonoid compounds as well as antioxidant capacity in flesh and greater total phenolc compounds and antioxidant capacity in peel than those treated with the AC.