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Quispe, who was appointed bishop by Pope Francis in 2018, was also investigated by the Vatican for alleged embezzlement of church funds. Ugaz said the Vatican looked into allegations that Quispe removed chairs from a church property to use in a chicken restaurant which was part of a chain that he was said to have had a financial interest in. "The chain is called Patas Arriba, a phrase meaning "upside down" but which literally translates as "legs in the air."

Journalist Paola Ugaz said that before he left office, Quispe was challenged by a group of people from the Aymara indigenous group who claimed he had misspent United Nations funds meant to support projects in their community. "He gave back money, which is rare in Peru, but it was because they threatened to lynch him and the Aymara are known for keeping to their word," she said.