Following years of attempts to discredit his legacy as a pioneer of micro-finance -- since copied the world over as a development tool -- the hounding has turned more personal and dangerous.
The perceived crime of the 73-year-old was to sign a joint statement along with three other Nobel laureates in April 2012 criticising the prosecution of gay people in Uganda.
Little remarked at the time, it has since been seized on by the Islamic Foundation, a government religious body, and amplified through tens of thousands of imams on its payrolls.
Protests have been held, leaflets calling him "an accomplice of Jews and Christians" have been distributed, and a "grand rally" has been called for October 31 in the capital Dhaka to denounce him.
"How can a state-run organisation run a campaign of criminal intimidation? It'll instigate violence against professor Yunus," Sara Hossain, a top lawyer and rights activist, warned in an interview with AFP.
The harassment has echoes of another movement against feminist writer and religious critic Taslima Nasreen who was forced to flee the country after being denounced like Yunus.
"It's unfortunate that he's facing the kind of campaign that I faced in 1994," Nasreen told AFP. "I was forced to leave the country because of the campaign by the fundamentalists, which the then government actively supported."
Yunus has been at odds with Prime Minister Sheikh Hasina since 2007 when he made a brief foray into the country's violent and polarised politics which is dominated by Hasina's family and her arch-rival Khaleda Zia.
Yunus's recent statement calling for free and fair elections in January 2014 is also thought to have angered her following changes to the electoral process and a crackdown on the opposition.
In 2011, he was forced out of the board of his beloved Grameen Bank by the central bank in a move widely believed to be orchestrated by the prime minister who accused him famously of "sucking blood from the poor".
Grameen Bank was set up by Yunus in 1983 to make collateral-free micro loans to rural and mostly women entrepreneurs. Its record in reducing poverty earned global fame and a Nobel Peace Prize for its founder in 2006.
Abul Kalam Azad, a spokesman for Hasina, rejected suggestions that the latest campaign against Yunus was directed by her. "She is not the DG (director general) of the Islamic Foundation," he told AFP.
The Islamic Foundation is part of the Ministry of Religious Affairs with a mandate to promote Islam.
Director General Shamim Mohammad Afzal told AFP that it was his "moral responsibility" as a Muslim and head of the organisation to take a stand against the man nicknamed the "banker to the poor".
"His statement has gone against the Koran and Hadith," Afzal told AFP, referring to the traditions of the Prophet Mohammad.
In speeches to clerics all over the country, Afzal has told them of their religious duty to protest Yunus's stand on homosexuality. One imam told AFP that he had been pressured to join rallies against his wishes.
The imam, who works in a southern district and asked not to be named, said clerics were asked to hold banners and distribute leaflets printed by the local Islamic Foundation office.
"Yunus has become an apostate for supporting homosexuality. He must publicly apologise, or we'll force him to leave the country like Taslima Nasreen," Maolana Moniruzzaman Rabbani, an organiser of anti-Yunus campaign, told AFP.
Rabbani is the secretary of a committee that helps run the state-funded national mosque in Dhaka and a deputy chief of an Islamic political party allied with the government.
Yunus, a former economics professor, declined several requests to be interviewed for this story.
He has found support in the politically polarised country in opposition parties who have rallied behind him after a government commission called for the state to take full control of Grameen Bank or dismantle it into 19 parts.
During a visit to the country in May last year former US Secretary of State Hillary Clinton also publicly supported Yunus, who is a personal friend of her and her husband Bill.
"I don't think they can force Yunus to leave the country," said Nasreen. "Unlike me, he has many powerful friends. But this campaign is going to bring a bad name for the country. No government should appease these fundamentalists."
Bangladesh is 90 percent Muslim. Although it is officially secular, Islam is the state religion.
Homosexuality is a crime punishable by a maximum life term but prosecutions are rare.
Early this year, the chairman of the state-run National Human Rights Commission (NHRC) called for a new law which would ban discrimination based on a person's sexual orientation and gender identity.