In 1997, Diskin was appointed commander of the Jerusalem District. During his tenure, the Shabak developed sophisticated operating methods, advanced technological and data mining capabilities, and by implementing them was able to debilitate Hamas's military wing in the Judea and Samaria area, which led to a major decline in the number of terrorist and suicide attacks in Israel. From 2000 to 2003, as the Shabak's Deputy Director, he implemented the use of advanced technological methods and operational doctrines. During the time of the Second Intifada, Diskin led the Shabak's activities in the field of counter-terrorism, developing operational capabilities and countermeasures against the suicide attacks, that had cost hundreds of lives. He also developed the doctrine of "Command and Control Operation Centers" (CCOC), in which he established a combined intelligence gathering, analysis and implementation process between the Shabak and different intelligence and security bodies in order to produce more accurate, actionable intelligence.