16 April 2026
CO26081 | Governing the Post-Jemaah Islamiyah Ecosystem in Indonesia
SYNOPSIS
Two years after the dissolution of Jemaah Islamiyah, the Indonesian experience shows that the end of a terrorist organisation does not eliminate the ecosystem that sustained it. Instead, the policy challenge shifts to governing the dispersed social infrastructures that once supported it.
COMMENTARY
The official dissolution of Jemaah Islamiyah (JI) on June 30, 2024, marked a historic milestone in Indonesia’s fight against terrorism. For more than thirty years, JI was the most influential jihadist group in Southeast Asia, responsible for a series of attacks, including the 2002 Bali bombings. Its leadership’s decision to formally disband the organisation was widely regarded as a strategic victory for Indonesia’s long-term counterterrorism (CT) efforts, especially those led by the Indonesian National Police’s anti-terrorism unit, Densus 88.
Research on extremist disengagement and terrorist organisational decline shows that disengagement processes often involve gradual social transitions rather than sudden ideological shifts. Even after formal structures collapse, organisations frequently leave behind durable infrastructures of relationships, narratives, and support networks; these were key to sustaining organisational ideology and membership. Studies of militant networks further suggest that these informal social infrastructures can persist long after formal organisational hierarchies have dissolved.
The Indonesian case now appears to be reaching this stage. Two years after JI’s dissolution, developments in 2026 indicate that the country has moved beyond dismantling a terrorist group and into a post-dissolution governance stage, overseeing educational institutions, social networks, and economic infrastructure historically linked to JI.
Mapping the Educational Ecosystem
A notable recent development has been the expansion in the number of educational institutions identified as historically affiliated with JI. In mid-2024, Indonesian authorities identified 42 pesantren (Islamic boarding schools) associated with the network, which together hosted an estimated 16,000 students. By February 2026, however, this figure had increased to about 120.
Much of this increase has not resulted from newly uncovered intelligence operations, but voluntary disclosure by pesantren administrators themselves. This process has been facilitated in part by the Forum Komunikasi Pondok Pesantren (FKPP), a coordination forum formed by JI pesantren. In January 2026, Ustadz Qosdi Ridwanullah, Chairman of FKPP, explained to this author that many administrators who had previously concealed their connections with JI had gradually chosen to disclose them publicly.
Pesantren leaders and administrators reported that joining FKPP gave them a sense of institutional visibility and protection when engaging with government institutions. As a result, some pesantren that had previously operated quietly have gradually emerged into the open, contributing to the expansion of the mapped institutional landscape.
This development reflects a broader transition from clandestine networks towards semi-open institutional engagement. Rather than being uncovered solely through coercive CT operations, parts of the JI educational infrastructure are emerging through negotiated disclosure and dialogue. Such voluntary acknowledgement represents a notable development in the sociology of extremist disengagement, in which trust-building between former networks and state institutions is a key mechanism facilitating the transition.
At the same time, the expansion from 42 to 120 institutions significantly alters the scale of the post-JI landscape. Educational institutions play a central role in the long-term reproduction of ideological environments. With thousands of students enrolled across these pesantren, each institution connects not only with its students but also with informal channels such as families, alumni networks, and broader community circles.
Voluntary Engagement by JI Pesantren – Opportunities and Challenges
The rapid growth in the number of identified institutions presents both an opportunity and a challenge. On the one hand, voluntary disclosure suggests that segments of the former network are increasingly willing to engage with the state. On the other hand, the expansion creates significant governance pressures. Monitoring and engaging with more than a hundred institutions and thousands of individuals raises questions about the state’s institutional capacity and long-term oversight.
These challenges are compounded by the social position of pesantren in Indonesian society. Islamic boarding schools occupy a respected cultural and religious role, and any perception that the state is intervening excessively in their affairs could generate political sensitivity. CT scholars have long noted that policies affecting religious institutions must be carefully calibrated to avoid reinforcing narratives of discrimination or state hostility towards a religious community. Managing this narrative dimension is, therefore, as important as addressing the security implications of the expanded landscape.
Furthermore, the mapped institutions likely represent only part of a broader ecosystem. Informal religious study circles, affiliated foundations, alumni networks, and business initiatives linked to former JI members may continue to operate outside formal mapping processes.
The State’s Integration Strategy
Recognising these complexities, Indonesian authorities have adopted a long-term engagement strategy to manage the transition following JI’s dissolution. This approach is guided by a five-year roadmap (2024-2029) structured into four phases and summarised as SIIP: Socialisation, Identification, Integration, and Participation.
The first phase centred on ensuring that former members understood the implications of the dissolution and the available pathways for disengagement. The second phase focused on mapping individuals, institutions, and networks linked to the organisation. By 2026, the roadmap had entered its third stage – integration – which has become the central policy priority.
One key focus involves facilitating the institutional normalisation of pesantren affiliated with JI. During early engagement meetings following the dissolution announcement, a recurring question from several former JI figures captured the psychological dimension of the transition: “We are ready to return to the Republic of Indonesia (NKRI). But is the Republic ready to accept us?” For many, dissolving JI was not merely tactical but the culmination of a long-standing aspiration to rejoin mainstream society.
In response, the Ministry of Religious Affairs emphasised that the state was prepared to accept their return and encouraged constructive participation. It outlined commitments to facilitate the granting of operational licenses, expand scholarship access, and enable access to government education funding.
However, developments on the ground reveal a more complex reality. Although the number of institutions linked to the former network has expanded significantly – from 42 to around 120 – this growth has not been matched by institutional licensing. Of these, only 21 pesantren hold official operating licenses, all obtained before JI’s dissolution.
Administrative requirements have proven to be a major obstacle. Regulations require a minimum land area, clear ownership, building permits, adequate facilities and sanitation infrastructure, a mosque, and the inclusion of classical Islamic texts. In practice, many affiliated pesantren struggle to meet these standards, slowing the licensing process.
Political developments within the Ministry of Religious Affairs have compounded these difficulties. Leadership changes following the dissolution triggered a reshuffle of senior officials responsible for pesantren affairs, disrupting early momentum behind policy commitments. At the same time, budget cuts across ministries constrained the ministry’s capacity to implement new programmes.
Recognising the risks of prolonged uncertainty, Densus 88 intensified coordination with the ministry. Following these engagements, the ministry re-restarted the licensing process through administrative readiness assessments.
The ministry has emphasised that it is seeking workable pathways to enable these institutions to obtain official status while complying with regulatory standards. Formal licensing would grant access to state support and enable curriculum guidance, supervision, and integration into the national education system.
Alongside institutional normalisation, authorities have also introduced economic empowerment initiatives targeting former JI communities. In Boyolali, Central Java, vocational training programmes were organised in collaboration with the Ministry of Agriculture and local authorities. The objective was to strengthen economic sustainability and reduce the risks associated with social marginalisation. These initiatives reflect a broader insight from disengagement research: Economic vulnerability and social exclusion can slow reintegration and reinforce isolation.
Conclusion
Developments around JI since its dissolution show a significant shift in CT policy. Although dismantling a terrorist group’s operational structure is a major success, it does not eliminate the social environments that sustained it. In Indonesia, two years after JI’s dissolution, a new phase has emerged, with the main challenge no longer being to defeat the group but to manage the networks that remain.
Educational institutions, alumni networks, community relationships, and economic livelihoods now require governance that combines security coordination, institutional integration, and socio-economic engagement. The Indonesian experience offers a broader lesson: Organisational dissolution should not be seen as the end of extremist movements, but as the beginning of a longer governance process.
About the Author
Khoirul Anam is a doctoral candidate in Political Science at the Indonesia International Islamic University (IIIU), specialising in security governance, political decision-making, and international reputation.
SYNOPSIS
Two years after the dissolution of Jemaah Islamiyah, the Indonesian experience shows that the end of a terrorist organisation does not eliminate the ecosystem that sustained it. Instead, the policy challenge shifts to governing the dispersed social infrastructures that once supported it.
COMMENTARY
The official dissolution of Jemaah Islamiyah (JI) on June 30, 2024, marked a historic milestone in Indonesia’s fight against terrorism. For more than thirty years, JI was the most influential jihadist group in Southeast Asia, responsible for a series of attacks, including the 2002 Bali bombings. Its leadership’s decision to formally disband the organisation was widely regarded as a strategic victory for Indonesia’s long-term counterterrorism (CT) efforts, especially those led by the Indonesian National Police’s anti-terrorism unit, Densus 88.
Research on extremist disengagement and terrorist organisational decline shows that disengagement processes often involve gradual social transitions rather than sudden ideological shifts. Even after formal structures collapse, organisations frequently leave behind durable infrastructures of relationships, narratives, and support networks; these were key to sustaining organisational ideology and membership. Studies of militant networks further suggest that these informal social infrastructures can persist long after formal organisational hierarchies have dissolved.
The Indonesian case now appears to be reaching this stage. Two years after JI’s dissolution, developments in 2026 indicate that the country has moved beyond dismantling a terrorist group and into a post-dissolution governance stage, overseeing educational institutions, social networks, and economic infrastructure historically linked to JI.
Mapping the Educational Ecosystem
A notable recent development has been the expansion in the number of educational institutions identified as historically affiliated with JI. In mid-2024, Indonesian authorities identified 42 pesantren (Islamic boarding schools) associated with the network, which together hosted an estimated 16,000 students. By February 2026, however, this figure had increased to about 120.
Much of this increase has not resulted from newly uncovered intelligence operations, but voluntary disclosure by pesantren administrators themselves. This process has been facilitated in part by the Forum Komunikasi Pondok Pesantren (FKPP), a coordination forum formed by JI pesantren. In January 2026, Ustadz Qosdi Ridwanullah, Chairman of FKPP, explained to this author that many administrators who had previously concealed their connections with JI had gradually chosen to disclose them publicly.
Pesantren leaders and administrators reported that joining FKPP gave them a sense of institutional visibility and protection when engaging with government institutions. As a result, some pesantren that had previously operated quietly have gradually emerged into the open, contributing to the expansion of the mapped institutional landscape.
This development reflects a broader transition from clandestine networks towards semi-open institutional engagement. Rather than being uncovered solely through coercive CT operations, parts of the JI educational infrastructure are emerging through negotiated disclosure and dialogue. Such voluntary acknowledgement represents a notable development in the sociology of extremist disengagement, in which trust-building between former networks and state institutions is a key mechanism facilitating the transition.
At the same time, the expansion from 42 to 120 institutions significantly alters the scale of the post-JI landscape. Educational institutions play a central role in the long-term reproduction of ideological environments. With thousands of students enrolled across these pesantren, each institution connects not only with its students but also with informal channels such as families, alumni networks, and broader community circles.
Voluntary Engagement by JI Pesantren – Opportunities and Challenges
The rapid growth in the number of identified institutions presents both an opportunity and a challenge. On the one hand, voluntary disclosure suggests that segments of the former network are increasingly willing to engage with the state. On the other hand, the expansion creates significant governance pressures. Monitoring and engaging with more than a hundred institutions and thousands of individuals raises questions about the state’s institutional capacity and long-term oversight.
These challenges are compounded by the social position of pesantren in Indonesian society. Islamic boarding schools occupy a respected cultural and religious role, and any perception that the state is intervening excessively in their affairs could generate political sensitivity. CT scholars have long noted that policies affecting religious institutions must be carefully calibrated to avoid reinforcing narratives of discrimination or state hostility towards a religious community. Managing this narrative dimension is, therefore, as important as addressing the security implications of the expanded landscape.
Furthermore, the mapped institutions likely represent only part of a broader ecosystem. Informal religious study circles, affiliated foundations, alumni networks, and business initiatives linked to former JI members may continue to operate outside formal mapping processes.
The State’s Integration Strategy
Recognising these complexities, Indonesian authorities have adopted a long-term engagement strategy to manage the transition following JI’s dissolution. This approach is guided by a five-year roadmap (2024-2029) structured into four phases and summarised as SIIP: Socialisation, Identification, Integration, and Participation.
The first phase centred on ensuring that former members understood the implications of the dissolution and the available pathways for disengagement. The second phase focused on mapping individuals, institutions, and networks linked to the organisation. By 2026, the roadmap had entered its third stage – integration – which has become the central policy priority.
One key focus involves facilitating the institutional normalisation of pesantren affiliated with JI. During early engagement meetings following the dissolution announcement, a recurring question from several former JI figures captured the psychological dimension of the transition: “We are ready to return to the Republic of Indonesia (NKRI). But is the Republic ready to accept us?” For many, dissolving JI was not merely tactical but the culmination of a long-standing aspiration to rejoin mainstream society.
In response, the Ministry of Religious Affairs emphasised that the state was prepared to accept their return and encouraged constructive participation. It outlined commitments to facilitate the granting of operational licenses, expand scholarship access, and enable access to government education funding.
However, developments on the ground reveal a more complex reality. Although the number of institutions linked to the former network has expanded significantly – from 42 to around 120 – this growth has not been matched by institutional licensing. Of these, only 21 pesantren hold official operating licenses, all obtained before JI’s dissolution.
Administrative requirements have proven to be a major obstacle. Regulations require a minimum land area, clear ownership, building permits, adequate facilities and sanitation infrastructure, a mosque, and the inclusion of classical Islamic texts. In practice, many affiliated pesantren struggle to meet these standards, slowing the licensing process.
Political developments within the Ministry of Religious Affairs have compounded these difficulties. Leadership changes following the dissolution triggered a reshuffle of senior officials responsible for pesantren affairs, disrupting early momentum behind policy commitments. At the same time, budget cuts across ministries constrained the ministry’s capacity to implement new programmes.
Recognising the risks of prolonged uncertainty, Densus 88 intensified coordination with the ministry. Following these engagements, the ministry re-restarted the licensing process through administrative readiness assessments.
The ministry has emphasised that it is seeking workable pathways to enable these institutions to obtain official status while complying with regulatory standards. Formal licensing would grant access to state support and enable curriculum guidance, supervision, and integration into the national education system.
Alongside institutional normalisation, authorities have also introduced economic empowerment initiatives targeting former JI communities. In Boyolali, Central Java, vocational training programmes were organised in collaboration with the Ministry of Agriculture and local authorities. The objective was to strengthen economic sustainability and reduce the risks associated with social marginalisation. These initiatives reflect a broader insight from disengagement research: Economic vulnerability and social exclusion can slow reintegration and reinforce isolation.
Conclusion
Developments around JI since its dissolution show a significant shift in CT policy. Although dismantling a terrorist group’s operational structure is a major success, it does not eliminate the social environments that sustained it. In Indonesia, two years after JI’s dissolution, a new phase has emerged, with the main challenge no longer being to defeat the group but to manage the networks that remain.
Educational institutions, alumni networks, community relationships, and economic livelihoods now require governance that combines security coordination, institutional integration, and socio-economic engagement. The Indonesian experience offers a broader lesson: Organisational dissolution should not be seen as the end of extremist movements, but as the beginning of a longer governance process.
About the Author
Khoirul Anam is a doctoral candidate in Political Science at the Indonesia International Islamic University (IIIU), specialising in security governance, political decision-making, and international reputation.
