Growth of 6-year old ‘Niitaka’ pear (Pyrus pyrifolia Nakai) trees and control of insect and disease occurrences were compared between fermented soybean extracts and rain-shelter system for two years. Foliar application of fermented soybean extracts was applied at 6 times as a pre-experiment in the open-field in 2013, with a rain-shelter system in 2014. Fermented soybean extract treatment increased foliar concentrations of approximately 0.46% T-N, 0.17% K, 0.19% Ca, and 0.06% Mg in 2013 compared to the control, with similar macro-nutrients between the control and soybean extract treatment observed in 2014. Rain-shelter system increased foliar concentrations of T-N, Ca, and Mg compared to the open-field. There were no significantly different between the control and soybean extract treatment for number of leaves per fruit, leaf dry weight, phytotoxicity, and completed shoot growth on August during the two years. Rain-shelter system increased leaf dry weight and did not affect phytotoxicity in the leaves. Fruit quality parameters were mostly similar to control and soybean extract treatment for two years, with higher fruit firmness observed for soybean extract treatment. Rain-shelter system advanced 4 days of harvest dates, and increased approximately 7.0 ton fruit yield per ha, 20 g mean fruit weight, and fruit soluble solid contents compared to open-field in 2014. Soybean extract treatment little suppressed occurrence of disease and insect on the leaves and fruits in both years. Rain-shelter system increased occurrence of Venturia nashicola on the leaves and to 63.8% of Gymnosporangium asiaticum on the fruits in 2014. Strong winds and storms in May elevated relative humidity in the rain-shelter system and caused high infection of the disease occurrence, requiring for an additional green control method. Soybean extract treatment little affected tree growth and would have initiated for a long-term study to evaluate tree physiological characteristics. Rain-shelter system improved fruit productivity and advanced harvest dates, which could have been more effective facility at a Thanks Giving Day between middle and end of September.