NEW DELHI — India’s crackdown on foreign aid will claim its most prominent casualty this month, as a Colorado-based Christian charity that is one of India’s biggest donors closes its operations here after 48 years, informing tens of thousands of children that they will no longer receive meals, medical care or tuition payments.

The shutdown of the charity, Compassion International, on suspicion of engaging in religious conversion, comes as India, a rising economic power with a swelling spirit of nationalism, curtails the flow of foreign money to activities it deems “detrimental to the national interest.”

More than 11,000 nongovernmental organizations have lost their licenses to accept foreign funds since Prime Minister Narendra Modi took office in 2014. Major Western funders — among them George Soros’s Open Society Foundations and the National Endowment for Democracy — have been barred from transferring funds without permission from Indian security officials.

But few have been as vocal about their struggle as Compassion International, which solicits donations through its $38-a-month “sponsor a child” program and distributes them through church-affiliated service centers. It has repeatedly ranked as India’s largest single foreign donor, transferring around $45 million a year.

Its executives vehemently deny the government’s allegation that it is funding religious conversions, and say India has given them no opportunity to rebut the accusation. Instead, they say they found themselves in murky back-channel negotiations with a representative of the Rashtriya Swayamsevak Sangh, or R.S.S., a right-wing Hindu ideological group that is closely connected with the governing Bharatiya Janata Party but that has no official role in governance.

A spokesman for India’s Ministry of Home Affairs, which oversees regulation of foreign charities, declined repeated requests for comment on the case.

A Foreign Ministry official, speaking on condition of anonymity, following diplomatic protocol, said that Compassion International’s partners were violating Indian law by engaging in religious activities, and that the organization declined a government offer to re-register as a religious organization, which would have allowed it to continue its work in India.

“What we hear from our friends in India is that it would be tragic if they were successful in shutting down Compassion, because that would leave other ministries very vulnerable,” Mr. Mellado said. “They are feeling like they’re next.”

That summer, income tax investigators began raiding offices affiliated with Compassion International, apparently seeking evidence that funds were being used to convert Indian families.

“They kept asking him, ‘Why did you have a spiritual component to the program? What do you do in the area of spiritual development?’” he said. “We said we teach moral values; we do not force anyone into religion.”

Compassion International executives learned early last year, from an item in an Indian newspaper, that their group had been added to the list of organizations whose transfers required prior permission by the Ministry of Home Affairs, said Stephen Oakley, Compassion’s general counsel.

In the United States, Mr. Mellado was pressing, with an increasing sense of urgency, for an opportunity to plead his case with Indian officials.

But the only interlocutors they could find were through unofficial channels. In October, a Washington-based representative of the R.S.S., Shekhar Tiwari, reached out to John Prabhudoss, who heads an umbrella organization of Indian-American Christians and has a long association with Compassion International and its leaders, Mr. Prabhudoss said.

Mr. Mellado said he was puzzled by the indirect outreach, but decided to give it a try.

“We are trying to navigate through understanding of the dynamics on the Indian side,” he said. “We understand that the B.J.P. and the R.S.S. are tied together somehow, so it seems to us that we also need to be talking to the R.S.S.”

Things went downhill quickly after that. In early January, Mr. Oakley, the general counsel, went to New Delhi to plead his case to India’s foreign secretary, Subrahmanyam Jaishankar, in a meeting also attended by the second-ranked United States diplomat in India.

As it came to an end, he said, a Home Ministry official suggested that Compassion International re-register its Indian partners as religious entities, a step that the charity’s legal team discouraged, saying it would lead to further paralysis.

“It was a very disingenuous offer,” Mr. Oakley said. “Either he didn’t know that was legally impossible, or it was an offer designed to end the meeting.”

Last week, word went out to the group’s 500 Indian partners that they would have to shut down their operations. Among them is Bethesda Charitable Endeavors, which funds a community center in a town called Haldwani, in the Himalayan foothills.

“I was heartbroken, because for the past six months, we were living in hope that something would happen,” he said. “Maybe a miracle.”

Already, 15,000 of the 145,000 Indian children regularly receiving services through Compassion International have been severed from the programs. Beginning on Friday, the sponsors will be contacted individually, at the rate of 2,500 per day, and asked to transfer their sponsorships from Indian children to children from other countries.

Priya Saxena, 13, is among the children who have been asked not to return to the community center in Haldwani.

Her father, a vegetable vendor, earns a monthly salary of about 1000 rupees, or around $16.

“Now I do not know what the future holds for me,” she said. “I hoped to become a doctor. But now that we are told we will no longer have sponsors to see us through the education, I don’t know what will happen.”

She added: “This place taught me to have a life. It is finished now.”