Amil Zakat Institution in Indonesia is spread over some provinces. The potention of zakat which is approximately about Rp 300 triliyun is not achieved yet because of people demand on accountability and transparantion from amil zakat institution itself. The complex problem that happen at now is because the lack of people trust on amil zakat institution itslef. Because of that, the object of this research is to know the effect of intern controlling implementation., the utilize of information technology, and total quality management on good governance application on amil zakat institution. The participants on this research are the employee of amil zakat institution which is located in Yogyakarta. The technique of data collecting is by spreading the questioners. The amount of questioners is 100 questioner. This research uses Partial Least Square (PLS) as the analysis tool because the data that can be processed are only 42 questioners. Based on analysis which had been done by the researcher, it can be concluded that intern controlling implementation., the utilize of information technology, and total quality management give the positive and significant effect on good governance application with the value of 51,6 % and the rest of it is from the variable outside of this research. The most effect variable on good governance apllication is the utilize of information technology.