According to local media reports and human rights groups, more than 700 people were arrested across five provinces during the 12-day conflict.
The Centre for Human Rights in Iran, which is based in New York, said it received credible reports of hundreds more arrested in Tehran.
It reported that at least six people were executed for spying for Israel, including three who were put to death in Oroumieh in western Iran on June 25.
Rights groups have condemned the moves, with Amnesty International warning against arbitrary executions and expedited trials.
The arrests have also raised fears inside Iran that a new wave of repression is coming, as the Government seeks to root out spy networks and clamp down on any dissent among the wider population.
Iranian security forces have beaten, arrested, tortured and executed thousands of people since the Islamic republic was founded in 1979.
More recently, the regime cracked down on nationwide protests that erupted when a woman died while in the custody of Iran’s guidance patrol - or morality police - in September 2022.
In the months leading up to Israel’s offensive, the Government appeared to ease some social restrictions, while others were tightened. The enforcement of strict female dress codes appeared to taper off in some cities, but the Government increased its monitoring of discourse online.
At the same time, Iranian prisons stepped up executions. At least 975 people were executed in Iran last year, according to the United Nations, which said it was the highest number recorded in nearly a decade.
So when the Israeli strikes started, 26-year-old Iman, an engineer from Tehran, said he immediately began to worry about a potential crackdown.
“As long as this government exists, I am concerned about the chances of increased repression, but during times when there’s an ‘external threat’, the repression gets much worse, as they have more excuse to see us as enemies,” he said of Iranian authorities.
Iman, like some others in this story, spoke on the condition that he be identified only by his first name for fear of reprisal by security forces.
Over the past week, he said, he has changed the way he dresses in public, wearing less colourful clothing out of fear he could become a target.
New checkpoints in Tehran, where plainclothes officers stop cars and question drivers, have contributed to an intimidating atmosphere in the sprawling capital, residents said.
Zahra, 41, an activist from Tehran, said she has heard that at least four fellow activists were rounded up during the conflict. She fears that more widespread arrests are on the horizon, she said.
“The Iranians probably don’t even know the full extent of the infiltration yet,” said a Western official who was briefed on the security situation.
“So, they are out there hunting,” the official said. “Suspicions are heightened.”
Perhaps most troubling, rights groups say, is the effort by parliament to make espionage a capital crime.
Iran is already one of the world’s top executioners, hanging people for offences ranging from murder and rape to drug smuggling and corruption.
The law would give the judiciary much broader authority to impose the death penalty, rights activists say.
And while Israel pummelled Iranian military targets throughout the conflict, including weapons, infrastructure, and senior commanders, the tools Iran uses to crack down domestically are largely intact, according to Afshon Ostovar, an Iran expert and professor of national security affairs at the Naval Postgraduate School in California.
“What Israel has done is really weaken the military as an external actor, but it hasn’t done much to weaken it as an internal actor. And it takes a lot less to wage violence inside a country than outside of it,” Ostovar said.
To crack down domestically, Iranian forces “don’t need missiles and drones and jets and helicopters. They just need rifles and big vehicles, and those still exist,” he said. “The state hasn’t lost its ability to monopolise violence.”
But Ostovar doubts that Iran’s leaders will reflect on some of the more uncomfortable questions about their deep unpopularity and the value of some security practices such as mass surveillance.
“If they were reflective, they’d realise that the reason why they were so bad picking up the Israelis is because they’re focused on every single person in the crowd,” he said.
He referred to surveillance programmes that cast wide nets, monitoring social media discourse or how Iranian women cover their hair in public.
“They have no way to discriminate who’s an actual spy and who’s not, because everybody with a bad hijab or tweeting the wrong thing is seen as equal to an actual foreign operative,” Ostovar said.
The Iranian judiciary announced last week that it was expanding its monitoring of electronic communications. Jahangir, the judiciary spokesman, said that it would also pursue online accounts “that were co-operating with the enemy”.
Jahangir also praised Iranian citizens, who he said “immediately provided a lot of information” that led to quick identifications and arrests.
In recent days, top Iranian officials have emphasised the country’s “unity” in the face of Israel’s attacks, which killed more than 900 people, according to the Government.
In his first public remarks since the ceasefire, Iran’s Supreme Leader, Ayatollah Ali Khamenei, said the country “showed that when it’s necessary, a unified voice will be heard from this nation, and praise God, this is what happened”.
President Masoud Pezeshkian echoed those comments. Iranians learned “not to submit to humiliation and not to bow our heads before oppression”, he said in a statement on X. “Our voice of unity reached the ears of the world.”
Regardless of the messaging, however, Iran has emerged from the conflict “in a greatly weakened position”, said Gregory Brew, an Iran analyst with Eurasia Group, a New York-based political risk consultancy.
“There will be questions about the strategic failures of not only the last two weeks, but of the last two years,” he said, referring to the collapse of Iran’s allies in Gaza, Lebanon and Syria following the Hamas attacks on Israel on October 7, 2023. That kind of accounting could lead to shuffles within the country’s leadership.
“So not regime change,” Brew said. “But changes within the regime should be expected in the months and years ahead.”