In 1978, following his mandatory military service, Diskin joined the Shabak and in the following years served in several operational positions in the Nablus district in the Judea and Samaria region, and in Beirut and Sidon during the 1982 Lebanon War. In 1984 he was appointed head of operations in the Nablus district and by 1989, the Jenin and Tulkarm districts, also in the northern Judea and Samaria area. During this time he was in charge of gathering and analyzing intelligence on the activities of terrorist groups in the area, and performing operations based on this intelligence.