The Federal Police’s Operation Bullish investigated irregularities in transactions carried out by the Brazilian Development Bank (BNDES) during JBS’s acquisition of the U.S. company Pilgrim’s Pride and the incorporation of the Bertin meatpacking plant, along with Swift Argentina, Swift USA, National Beef, and Smithfield. The investigation, as reported by the Federal Public Prosecutor’s Office (Ministério Público Federal – MPF), indicated that JBS obtained public funds more easily after hiring consultants linked to former Finance Minister Antonio Palocci, in a scheme that also involved BNDES employees. In December 2019, the MPF requested compensation for damages caused by JBS and BNDES employees, totaling more than 21 billion Brazilian reais (around US$ 6.4 billion at that time). In 2024, however, Brazil’s Federal Court of Auditors (Tribunal de Contas da União – TCU) concluded that there was no evidence of irregularities in the bank’s operations.

JBS and other companies in the sector were investigated for a scheme to bribe meatpacking inspectors, as part of Operation Carne Fraca from the Brazilian Federal Police. The scheme allowed the sale of rotten meat, the falsification of export documents, and deliberate failures in the inspection of meatpacking plants. The accusations against the companies included the use of chemicals to disguise spoiled meat, which led to a series of suspensions of Brazilian meat imports in multiple countries.

The Brazilian Federal Police’s Operation Cui Bono investigated loans granted by Caixa Econômica Federal to various companies, including Eldorado Celulose, owned by J&F Investimentos, the holding company of JBS. According to the Federal Public Prosecutor's Office, a group of politicians authorised loans from Caixa in exchange for bribes paid by the benefiting companies. Among the J&F facilitators were former minister Geddel Vieira Lima and former president of the Chamber of Deputies Eduardo Cunha.

As reported by O Globo, the Brazilian Federal Police’s Operation Greenfield investigated Eldorado Celulose, a company owned by J&F Investimentos—the holding company of JBS—for signs of irregularities in the selection of companies to receive investments from pension funds. The suspicion was that those responsible for the investments acted illicitly and paid overvalued amounts for the financed assets. The operation resulted in an agreement in which the group undertook to compensate the pension funds for the losses. Six years later, in 2023, Supreme Federal Court (STF) Justice Dias Toffoli suspended the payment, following a request from J&F to “correct abuses” in the process.

The Brazilian Federal Police launched Operation Sépsis, an offshoot of Operation Car Wash (Operação Lava Jato), which involved a company owned by J&F Investimentos, the holding company that controls JBS. Police carried out search and seizure warrants at the headquarters of Eldorado, the group’s pulp company, and also searched the São Paulo mansion of Joesley Batista, one of the owners of the holding company. It was reported that Eldorado was suspected of having received favorable treatment in loan approvals from the FI-FGTS, a fund managed by Caixa Econômica Federal, Brazil’s state-owned bank.

JBS has been the target of several labor lawsuits by Brazil’s Labor Prosecutor’s Office (Ministério Público do Trabalho – MPT) over a lack of safety and accidents that occurred in its meatpacking plants, according to Repórter Brasil. The report states that one worker had his arm caught in a machine during cleaning operations in Mato Grosso do Sul state, another had his hand severed in a pig grinder in Paraná state, and a mechanic died after falling into a grinding machine in São Paulo.