KrilMohd's blog: Documented Cases: Compromised Nonprofits in Abuse Scandals.

A U.S. nonprofit contracted by the Department of Health & Human Services to shelter unaccompanied migrant children faced serious allegations:

From at least 2015, staff were accused of patterns of sexual abuse, harassment, rape, solicitation of nude photos, and coercion of minors in their care.
The U.S. Department of Justice filed a civil rights lawsuit in July 2024 citing "severe or pervasive sexual harassment." When HHS stopped sending children to their shelters, DOJ dropped the lawsuit. All children were moved elsewhere.

Once praised as a heroic anti-trafficking nonprofit behind the film Sound of Freedom, OUR came under scrutiny for:

Allegedly exaggerating or fabricating involvement in child rescue operations to raise funds.
Investigations by local authorities and media revealed no evidence of the claimed arrests, and OUR had paid public law enforcement agencies substantial donations.

Intended to empower vulnerable Liberian girls through education:

Co-founder Macintosh Johnson, supported and enabled by the charity, systematically raped and abused students under its care.
Despite rumors and warning signs, the organization continued operations and mismanaged the crisis before Johnson’s arrest.

An Islamic-affiliated conglomerate that operated dozens of “welfare homes” in Malaysia and overseas:

Over 600 children (aged 1–17) were rescued from facilities where they endured sexual violence—including sodomy—physical punishment, and indoctrination.
More than 400 people, including the CEO, were arrested; assets were frozen and properties seized.
For years, state agencies ignored or suppressed dozens of complaints, allowing the abuse to continue.

Formerly supported children in care and child migration programs:

The charity paid secret settlements to survivors of abuse in its institutions, only publicly admitting to this in 2017 under pressure from the Independent Inquiry into Child Sexual Abuse (IICSA).
Victims suffered for decades before institutional accountability arrived.

Other Notable Examples

The Refuge Ranch, a Texas-based faith facility for survivors of trafficking, was shut down in 2022 after investigations uncovered medical neglect, sexual abuse, forced nude photography, and exploitation of girls aged 11–17.
Kids Company (UK) collapsed in 2015 amid financial scandal and unsubstantiated allegations of sexual abuse (though later investigations found no criminal wrongdoing). The fallout revealed failures in oversight and safeguarding.