Nurses and caregivers at Palomar Health held a picket protest on October 10, 2024, demanding improved staffing levels, safer working conditions, and better patient care. The protest highlighted severe labor issues including 12-hour shifts without proper breaks and a significant attrition rate, with nearly half of the staff having left in the past two years. Palomar Health has not commented on the matter.

On May 5, 2024, Palomar Health Medical Group experienced a cybersecurity incident affecting its Poway and Escondido facilities. Suspicious activity led to unauthorized access and potential copying of files containing sensitive patient data, prompting class action lawsuits and raising concerns about inadequate data protection measures.

An anonymous complaint filed with the California FPPC alleges that Palomar Health's 15‐year management services agreement with Mesa Rock Health Care Services involved potential conflicts of interest, with CEO Diane Hansen and contract lawyers accused of having inappropriate financial interests. The complaint also raises issues over alleged violations of public meetings laws, prompting concerns about transparency and public accountability, even as Palomar defends its board-approved actions and cites legal precedent.

Board members at Palomar Health raised concerns that board chair Linda Greer had a conflict of interest in renewing the contract with Emergent Medical Associates after receiving significant campaign contributions from related parties. Critics argue that her failure to recuse herself undermines democratic governance and breaches the organization’s ethical standards.

Palomar Health’s top executives and associated groups contributed significant campaign funds to specific board candidates ahead of elections. This move, which came on the heels of controversial staffing and contracting changes, has raised concerns over conflict of interest and undue influence over the board’s decisions.

Palomar Health's executive leadership and the founder of Emergent Medical Associates made significant campaign contributions to board candidates who supported a controversial contracting change. This move has raised concerns about corporate influence over democratic board elections in a public healthcare district.

Palomar Health executives, including top leadership figures, were criticized for financially supporting specific board candidates who backed a controversial contract change with Emergent Medical Associates. The donations, which included a $9,000 contribution to incumbent board chair Linda Greer and similar support for other candidates, have raised concerns about transparency and potential conflicts of interest within the hospital's governance.

Nurses and caregivers at Palomar Health announced a one-day unfair labor practice strike on June 23, protesting management’s refusal to negotiate a fair contract and unsafe staffing decisions that endanger patient care.

In 2021, during collective bargaining negotiations, Palomar Health filed a lawsuit accusing union organizers of trespass and unlawful picketing, seeking to ban them from hospital premises. The move was legally challenged by the unions, which argued that such actions violated their rights under the Meyers-Milias-Brown Act. The Court of Appeal later ruled in favor of the unions, emphasizing that their organizing activities were protected.