Turkish Hezbollah's situation greatly changed in the mid 1990's, as PKK's threat to Turkey waned, culminating in a 1999 truce. With the government's focus away from PKK, Turkish Hezbollah arose as a target for the Turkish government, who began to arrest its members. The lack of PKK as a serious adversary also caused Turkish Hezbollah to change its focus, and in the mid-1990's it began to target secular academics and journalists, feminists and religious Muslims who did not support its goal of establishing an Islamic state in Turkey. Full-scale operations against the group by the Turkish government began in 2000, resulting in the deaths of hundreds of militants throughout southeastern Turkey. Turkish police, investigating the fraudulent use of a kidnapped businessman's credit card, were led to small house in the city of Beykoz, where a shootout ensued and the group's leader, Huseyin Velioglu, was killed. Also captured in the raid were chief lieutenants Edip Gumus and Cemal Tutar. This raid, which yielded a wealth of information on the group and led to the capture of other key members, is seen as the beginning of the end of Turkish Hezbollah. Many of its remaining members have escaped to Iran and Iraq. However, involvement of Turkish Hezbollah is suspected in the 2003 bombings of synagogues and British targets, although the links are unclear at this point.

Like with Turkish Hezbollah, Turkish Islamic Jihad is believed to be financed by Iran yet not directly related to the Islamic Jihad group carrying out attacks in Israel and the Occupied Territories.  The group has never publicly declared a specific ideology, but their name implies a fundamentalist Islamic orientation.  In their only public statement, the group claimed to oppose the efforts of both the United States and Egypt at the 1991 Madrid Peace Conference, whom they accused of attempting to "divide up the Middle East."

Although they have not claimed an attack sine 1996, the Turkish Islamic Jihad was mentioned in the Iranian press as late as 2000 as one of a number of groups continuing to "carry out clandestine political and military activities."  The group is presumed to be inactive; however the Islamist movement continues to present a threat to Turkey.