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.

According to the Regional Labor Court of Mato Grosso state (TRT/MT), JBS was ordered by the Labor Court to pay R$2.3 million (around US$ 1 million at the time the fines were issued) due to labor violations at its meatpacking plant in Juruena, in the state of Mato Grosso. These included supplying employees with meat containing maggots. The lawsuits, filed by the Labor Prosecutor’s Office (Ministério Público do Trabalho – MPT), cited issues such as exhausting working hours, lack of protective equipment, and the absence of mandatory occupational health programs. As reported by the MPT/MT, in 2016 the company signed an agreement to pay R$3 million (around US$ 900,000 at that time) in compensation for collective moral damages to settle this and other lawsuits related to working conditions at its facilities in Mato Grosso.