IntelBrief: The Past, Present, and Future of Al-Qaeda in Afghanistan and Pakistan

Abdul Sayed
6 min readAug 20, 2021


Abdul Sayed

Bottom Line Up Front

  • Al-Qaeda has not been eliminated from the Afghanistan-Pakistan (AfPak) region, and the group still enjoys significant support in the broader regional jihadist landscape.
  • To counter the aggressive U.S. counterterrorism campaign, al-Qaeda altered its organizational structure and strategy in AfPak, strengthening its roots in the region to ensure its survival.
  • Through this localization strategy, al-Qaeda achieved its primary goal in the region-depriving the U.S. of military victory over the Taliban, leading to the re-establishment of the Islamic Emirate of Afghanistan.
  • Despite U.S. pressure, the Taliban has refused to sever its relationship with al-Qaeda, which will create serious problems for the region now that the Taliban is back in power in Afghanistan.

In the last two decades, massive efforts of the so-called Global War on Terror (GWoT) in the Afghanistan-Pakistan (AfPak) region resulted in severe blows to al-Qaeda. However, the group maintains deep, covert roots in the AfPak’s jihadist landscape, ensuring its longevity in the region. Since the al-Qaeda attacks of September 11, 2001, the U.S. has intensely focused on neutralizing al-Qaeda leadership and destroying its external operations planning capabilities. The first severe blow to al-Qaeda was the killing of its military chief and Osama bin Laden’s deputy, Mohammed Atef, in a U.S. airstrike in November 2001. The most recent major blow was in July 2015, when a U.S. drone strike eliminated Shaikh Umar Khalil, who served as second in command to al-Qaeda’s current emir Ayman Al-Zawahiri. Yet, even with these and many other tactical successes, al-Qaeda has not been defeated in AfPak, and the group enjoys significant support in the regional jihadist landscape. Its goal of rebuilding will be easier with the Taliban in control of Afghanistan.

To survive the post-9/11 U.S. counterterrorism onslaught, al-Qaeda engineered a strategic transformation in AfPak, strengthening its roots throughout the region. By doing so, al-Qaeda turned the U.S. invasion of Afghanistan into a golden opportunity. This is evident by al-Qaeda’s political strategy in the region. Al-Qaeda shifted focus from global terrorist attacks and external operations to supporting local jihadist groups throughout South Asia, and fueling the narratives that underpin their objectives. This shift helped build resilience, allowing al-Qaeda to survive despite the massive blows inflicted by the United States and its allies. Although U.S. counterterrorism operations focused on eliminating al-Qaeda leadership and foiling its transnational terrorist plans, the group cemented its relations with the local AfPak jihadist scene by appealing to the principles on which the group was initially founded. Al-Qaeda was established in 1988 as an international organization dedicated to ultimately restoring Islamic governance and the imposition of their interpretation of Sharia and removing Western influence from the Arabian peninsula. To achieve this goal, the organization launched training camps to mobilize militants and strengthen jihadist uprisings, efforts that eventually led to the 9/11 attacks. Following the U.S. invasion in 2001, Afghanistan was no longer a viable al-Qaeda sanctuary, and the group dispersed its fighters throughout AfPak in an attempt to avoid further harm from U.S. counterterrorism operations. This structural reconfiguration caused al-Qaeda to increasingly rely on local allies to advance its regional goals, resulting in the growth of various franchise groups.

Al-Qaeda’s post-9/11 resilience in AfPak results from its three-pronged regionalization strategy. First, al-Qaeda helped the Afghan Taliban establish a solid resistance base against the U.S. and allied forces, leading to a Taliban resurgence in the years immediately following the invasion. For this purpose, al-Qaeda relied upon loyalists from its Pakistani jihadist allies, including battle-hardened Kashmiri jihadists and sectarian militants from the Sunni militant group Lashkar-e-Jhangvi (LeJ). These Pakistani jihadists were enraged by the U.S. invasion of Afghanistan and Islamabad’s support for the U.S. Their nexus grew inextricably linked, and Pashtun tribal militants provided crucial safe havens for al-Qaeda militants on the Pakistani side of the AfPak border. Through military, political, and economic support, and through relationships with Afghan and Pakistani jihadists, al-Qaeda helped reshape the Afghan battlefield. Al-Qaeda accepted a subsidiary role to the Afghan Taliban in the post-9/11 insurgency and helped the Taliban maintain its monopoly on power in longtime Afghan strongholds. This helped al-Qaeda prove its unconditional loyalty to the Afghan Taliban, a favor that was returned when al-Qaeda lost its sanctuaries in Waziristan in 2015 and the Afghan Taliban again provided them shelter inside Afghanistan.

Secondly, al-Qaeda organized its post-9/11 Pakistani loyalists into the deadliest jihadist threat against the Pakistani state known as the Tehrik-e-Taliban Pakistan (TTP). The TTP served as al-Qaeda’s first line of defense in the region and still publicly declares its loyalty to Osama Bin Laden and his jihadist ideology. Al-Qaeda maintains influence over the TTP, as evidenced by its covert role in the TTP’s reunification process last year. Although TTP has mostly limited its operations to Pakistani soil, it echoes the al-Qaeda global jihadist agenda from a local perspective, a narrative that continues to resonate among pockets of the Pakistani population.

The third significant al-Qaeda achievement in AfPak was establishing its regional franchise in 2014, al-Qaeda in the Indian Subcontinent (AQIS), comprised of its post-9/11 Pakistani cadres. The al-Qaeda senior leadership handpicked these Pakistani cadres from its thousands of post-9/11 loyalists and groomed them over the years for the group’s future leadership responsibilities. This further helped al-Qaeda camouflage itself in the region, as AQIS cadres are difficult to identify among the thousands of jihadists active in the Afghan battlefield.

Through this localization strategy, al-Qaeda gradually turned its economic and human resources from transnational attacks into strengthening the Taliban insurgency in Afghanistan. The Bin Laden documents also reveal that al-Qaeda channeled much-needed funds to the Afghan Taliban for its war in Afghanistan. The al-Qaeda media, military, and guerilla warfare experts from Waziristan imparted advanced training to the Afghan Taliban. Al-Qaeda deployed its Pakistani allies and affiliates to fighting alongside Taliban units operating inside Afghanistan. This strategy finally led to its primary goal in the region-to deprive the U.S. of military victory over the Taliban, leading to the re-establishment of Taliban rule in the country.

Despite U.S. pressure during last year’s peace talks in Doha, the Taliban avoided making any promise to deny space to al-Qaeda in the future. This stance was also echoed in an Afghan television network’s recent interview with Taliban senior leader Amir Khan Muttaqi. When asked about the group’s future policies regarding al-Qaeda, Muttaqi said that the Taliban will never create enmity with al-Qaeda on behalf of the U.S. The Afghan Taliban central spokesman, Zabihullah Mujahid, also stated in an interview with an Afghan news channel that the Doha deal does not put any obligations on the Taliban for cutting ties with al-Qaeda. According to Mujahid, the only Taliban promise is that it will not let anyone use the Afghan soil against the U.S. and its allies. However, two reasons leave few doubts about whether al-Qaeda will again use Afghanistan in the future for any such actions that might threaten the survival of the Taliban’s future Islamic government in Afghanistan. First, the United Nations Security Council claims that the Taliban kept al-Qaeda onboard regarding its peace deal with the U.S. Secondly, al-Qaeda’s military and media strategies in AfPak demonstrate that al-Qaeda is fully committed to backing the Taliban. Additionally, Usama Mahmood, the leader of AQIS since 2019, following the killing of its founding emir Shaikh Asim Umar, told his group members that they should prepare for important responsibilities after the U.S. withdrawal from Afghanistan.

President Joe Biden, in his recent statement on the withdrawal of U.S. troops from Afghanistan, said that the United States’ main goal in Afghanistan was killing bin Laden and eliminating al-Qaeda’s capacity for attacking the U.S. Bin Laden has been dead for a decade, but al-Qaeda still maintains a strong presence in Afghanistan and Pakistan. Al-Qaeda does not need Afghanistan for any attack against the U.S. and its allies-it has strongholds throughout the region-but should the Taliban again provide a safe space, political cover, and training grounds, there is cause for concern that Al-Qaeda could once again plan attacks against the West. The group’s silence as U.S. troops withdraw and the Taliban rises to power should not be taken for granted. It might just mark the beginning of a new era for al-Qaeda.

Abdul Sayed is an independent researcher on jihadism and the politics and security of the Afghanistan-Pakistan region. Sayed has a master’s degree in political science from Lund University, Sweden. He is currently working on projects related to violent extremist organizations and transnational jihadism in the Afghanistan-Pakistan region. Twitter: @abdsayedd

Originally published at on August 20, 2021.



Abdul Sayed

I am a research analyst focusing on jihadism, Afghanistan, and Pakistan.