Iran’s Shadow War In Afghanistan: Proxy Forces, Political Sabotage, And Refugee Exploitation

Afghanistan - Iran border crossing. Photo Credit: Tasnim News Agency

This piece originally appeared in EURASIAREVIEW on July 14, 2025

For over four decades, Iran has played a complex and often destructive role in Afghanistan’s political, ethnic, and religious landscape. While publicly promoting Islamic solidarity and neighborly relations, Tehran has consistently undermined Afghan sovereignty through a mix of hard and soft power: supporting proxy militias, manipulating ethnic divisions, sabotaging central governments, and exploiting Afghan refugees as pawns in its regional strategy.

This article explores Iran’s covert war in Afghanistan—from its ideological meddling during the Soviet occupation to its use of militias, its toxic influence on Afghan politics, and its inhumane treatment of Afghan refugees living in Iran.

I. Historical Foundations: Brotherhood or Strategy?

Iran and Afghanistan share some historical, linguistic, and cultural ties. The easter regions of Iran—including Sistan was once part of Afghanistan, and Iran was once part of the Afghan Hotaki empire. Because of the decades of war and instability in Afghanistan, Iran has even tried to list globally renowned Afghan scholars and heritage after its name.

However, beneath some cultural affinity lies a stark geopolitical reality: Iran has never viewed a strong, independent, and unified Afghanistan as being in its strategic interest. Instead, its foreign policy has consistently aimed at keeping Afghanistan weak, fragmented, and dependent—a buffer zone between Iran and the competing interests of Pakistan, Saudi Arabia, and the United States.

II. 1980s: Exporting the Revolution and Sponsoring Shia Militias

After the 1979 Islamic Revolution, Iran under Ayatollah Khomeini adopted a revolutionary foreign policy: export Shiism and oppose Western and Sunni Gulf influence in the region. The Soviet invasion of Afghanistan (1979–1989) created the perfect vacuum for Tehran to spread its ideological and military footprint.

Iran’s Primary Tools:

Hezb-e Wahdat: A Shia-dominated Hazara militia, trained and funded by the Iranian Revolutionary Guard Corps (IRGC).

Cultural infiltration: Seminaries in Qom and Mashhad began hosting Hazara clerics and youth for indoctrination.

Splinter strategy: Iran backed smaller Shia factions to keep them divided and dependent.

While the U.S., Pakistan, Egypt, China, Europeans and Saudi Arabia funded Sunni mujahideen like Gulbuddin Hekmatyar and Burhanuddin Rabbani, Iran focused its attention on Shia minorities—particularly the Hazaras. But this support was never altruistic. These groups became Iran’s ideological proxies, loyal to Tehran more than to Kabul.

III. 1990s: Iran vs. the Taliban—The Northern Alliance Nexus

The post-Soviet civil war in Afghanistan opened a new chapter in Iran’s shadow war. The Taliban emerged in 1994 as a Sunni movement backed by Pakistan and Saudi Arabia, who once backed Jumiat Islamic led by Burhan-ud-Din Rabbani and Ahmad Shah Massoud. Iran saw the Taliban’s Deobandi ideology and Wahhabi sympathies as an existential threat, especially due to their persecution of Shias and Hazaras.

Tehran’s Response:

Formed a strategic alliance with the Northern Alliance (United Islamic Front).

Funneled weapons, training, and funds to leaders such as:

Ahmad Shah Massoud (Tajik)

Abdul Rashid Dostum (Uzbek)

Karim Khalili and Mohammad Mohaqiq (Hazara)

Iran, along with India and Russia, backed these warlords to contain the Taliban. However, the Northern Alliance was also implicated in war crimes, civilian massacres, and regional fiefdoms, further fracturing Afghanistan along ethnic lines.

Iran’s role during this time did not strengthen Afghan unity or sovereignty. Rather, it deepened ethnic polarization and fueled a civil war that cost hundreds of thousands of lives.

IV. 2001–2014: Iran’s Double Game in Post-Taliban Afghanistan

After the U.S. invasion in 2001 and the fall of the Taliban, Iran initially appeared to support the new democratic government. It participated in the Bonn Conference and pledged millions for reconstruction. Yet, this was a mask for a more insidious agenda.

Dual Strategy:

Public Diplomacy and Cultural Investment only to promote the Iranian cultural influence.

Built mosques, hospitals, and media stations in western Afghanistan based on the same policy, Iranian influence.

Promoted Shia education, Persian-language schools, and IRGC-friendly NGOs.

Funded politicians, journalists, and clerics sympathetic to Iranian interests.

Covert Sabotage:

Supported insurgent groups, including Taliban factions in Herat, Farah, and Nimroz to pressure U.S. forces.

Channeled money to warlords and ex-Northern Alliance members, weakening central authority.

Flooded Afghan markets with Iranian goods, further eroding Afghan self-sufficiency.

U.S. and Afghan intelligence regularly reported Iranian IEDs and weapons being used against NATO forces. Tehran was playing both sides: supporting the Afghan government in Kabul and its enemies in the countryside.

V. The Fatemiyoun Division: Afghan Refugees as Canon Fodder

One of Iran’s most morally reprehensible actions was the creation of the Fatemiyoun Division—a Shia militia composed almost entirely of Afghan Hazaras. Formed in 2012 by the IRGC’s Quds Force, it was deployed to fight for the Assad regime in Syria.

Recruitment Methods:

Targeted undocumented Afghan refugees in Iran.

Promised legal residency, money, and protection.

Threatened deportation for those who refused.

Made the Hazara leaders including Karim Khalili, Mohaqeq and Sarwar Danish to create and lead the Fatimyoun groups inside Afghanistan.

According to Human Rights Watch and other observers, thousands of impoverished Afghan youths were coerced into fighting a war they didn’t understand in a country they had never seen. Many were killed and buried without ceremony; others returned to Afghanistan deeply traumatized, creating security and social tensions.

This use of refugees as disposable proxies is a stain on Iran’s legacy and a violation of international law.

VI. 2014–2021: Closer Ties With the Taliban

As ISIS-K began targeting Shias and Iranian interests in Afghanistan, Tehran recalibrated its strategy—engaging directly with the Taliban, the very force it once sought to annihilate.

New Pragmatism:

Taliban leaders were invited to official talks in Tehran.

Iran began providing weapons, logistics, and safe haven to Taliban commanders operating in western Afghanistan.

The goal was to:

Counter ISIS-K.

Harass U.S. and NATO forces.

Maintain influence in a post-American Afghanistan.

Reports from Afghan intelligence showed that the Taliban used Iranian soil to rest, regroup, and launch operations. This support gave the Taliban strategic depth in western Afghanistan and increased their leverage in the Doha peace talks.

VII. 2021–Present: Taliban Rule and Iran’s Border Diplomacy

When the Taliban seized Kabul in August 2021, Iran adopted a cautious but transactional approach. Though it never formally recognized the Taliban, it kept its embassy in Kabul open and initiated diplomatic channels.

Tensions Persist:

Clashes along the Helmand River due to water disputes escalated into gunfire.

Iran has continued to support Shia militias in Bamyan, Daikundi, and parts of Herat.

Tehran also hosts exiled warlords and political figures, including Ismail Khan and other anti-Taliban elements, keeping its options open for future power shifts in Afghanistan.

VIII. Systematic Humiliation of Afghan Refugees

Perhaps the most visible and enduring example of Iran’s abusive policies is its treatment of Afghan refugees, who number about 5 million. For decades, Iran has used Afghan migrants as both cheap labor and geopolitical leverage.

Living Conditions:

Most Afghans live in legal limbo, denied the right to own property, drive vehicles, or enroll in schools, receive blood transfusion if required, even can’t purchase breads from the Iranian bakeries, while forced to work but not paid.

Children are often denied education unless they pay heavy fees or obtain temporary permits.

Refugees are regularly subjected to harassment, racism, and police brutality.

Deportations:

Iran has deported hundreds of thousands of Afghans, often without due process or warning.

Deportees report being beaten, robbed, and humiliated by border guards.

Iran uses deportations as a pressure tactic on the Afghan government and Taliban alike.

Institutionalized Racism:

Iranian media and public discourse often portray Afghans as criminals or parasites.

Employers exploit them as slave labor, refusing to pay wages under threat of deportation.

In times of economic hardship, Afghans are scapegoated, arrested, and publicly humiliated.

IX. Why Iran’s Role Must Be Confronted

Iran’s actions in Afghanistan are not those of a concerned neighbor or cultural ally. Rather, they are the actions of a regional hegemon exploiting instability for strategic gain.

Iran has:

Backed militias over governments.

Weaponized ethnic and sectarian divides.

Turned refugees into mercenaries.

Destabilized every post-2001 Afghan administration.

While other regional powers—Saudi Arabia, even Russia—bear their share of blame, Pakistan’s and Iran’s uniquely duplicitous and exploitative policies have done lasting damage to Afghan national unity, security, and dignity.

Conclusion: Afghanistan Deserves Better

For decades, Iran has spoken the language of fraternity while practicing the politics of domination. Its support for militias, manipulation of Afghan refugees, and cynical engagement with both democratic and extremist forces reveal a consistent aim: keep Afghanistan weak, divided, and dependent.

True regional peace will only come when Afghan sovereignty is respected, when refugees are treated with dignity, and when the proxies of foreign powers are replaced by the voice of the Afghan people themselves. Finally, it’s important to note that 95% of Afghan refugees in Iran are non-Pashtuns, often guided and influenced by their self-proclaimed leaders who openly admit to being under Iran’s control. These millions of Afghans need to realize that they have no genuine connections with Iran. Furthermore, they should stand up against their so-called leaders, including all Hazara leaders and most members of the Northern Alliance, who have exploited them for Iran’s benefit.