After the Amazon expedition of the 1870s, Rodrigues became discouraged over the difficulty of funding another expedition and briefly detoured into business, running a chemical factory. Not long afterwards, he was tasked to organize and direct a brand-new Botanic Museum of the Amazon in Manaus, which opened in 1883 under the sponsorship of Princess Isabel. He founded a journal, "Vellosia" (named in honor of José Mariano de Conceição Vellozo), to showcase the museum's work; it was discontinued after only four volumes were issued. Despite its royal patronage, the museum struggled financially and closed in 1890 when Rodrigues moved on to become director of the Botanic Garden of Rio de Janeiro, a position he would hold until his death. At the height of its development, the Botanic Museum of the Amazon had held some 10,000 botanical specimens, nearly all of which were lost on the museum's closure.