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The increasing of food demand in Indonesia affects farmers to use chemical fertilizer in order to increase agriculture productivity. However, chemical fertilizer could cause land fertility degradation when continually and inefficient use. One of solutions to overcome this problem is by using organic nanofertilizer that can be made from fish feed industrial waste which is abundant and unutilized. In addition, processed by sonication using ultrasound technology to speed up protein degradation. The aim of this study was to observe the effect of sonication temperature and time on protein degradation of fish feed industrial waste as raw materials of organic nanofertilizer. In this work, completely randomized design factorial with two factors were used. The first factor was temperature (40°C, 50°C and 60°C) and the second factor was time (45, 55 and 60 minutes). The effect was examined by protein solubility, percentage of nitrogen, phosphor, sodium and organic carbon. The best treatment was chosen, then compared with control (no treatment) based on pH, DO, BOD and particle size measurements. The result has shown that all factors and interaction between them have a significant effect on protein degradation of waste, but percentage of nitrogen, phosphor, sodium and organic carbon did not change significantly upon the sonication treatments. Major impact had treatment with 60°C for 65 minutes. It affected in decreased particle size but stay constant in value of pH, DO and BOD.