In 1865, he took part in his mentor's 1865 expedition to Brazil in search of evidence of an ice age there, which Agassiz later claimed to have found. After returning to Massachusetts, chronic ill health caused him to return to his family farm in Springfield. By 1867, Allen's health had improved enough that he went on a flurry of collecting trips, including at Sodus Bay, and in Illinois, Michigan, and Indiana. Upon his return to Massachusetts, he took the position of curator of birds and mammals at Harvard's Museum of Comparative Zoology. In the winter of 1868–1869, he was one of two ornithologists, the other being Charles Johnson Maynard, to explore the relatively unknown state of Florida, which was still very much a wilderness in the late 1860s. When he returned, he wrote a celebrated analysis of his trip entitled On the Mammals and Winter Birds of Eastern Florida, which was published in 1871. That same year he was elected a Fellow of the American Academy of Arts and Sciences. For the next few years, Allen ventured to the Great Plains, Rocky Mountains, and Dakota Territory on collecting trips for Harvard's museum. Except for an 1882 collecting trip in Colorado with fellow ornithologist William Brewster, Allen never went field collecting again, primarily because of his fragile health.
Following the end of his field-collecting days, Allen dedicated his life to research and editorial publication. In the early summer of 1876, Allen was elected by the Nuttall Ornithological Club to replace Charles Johnson Maynard and Henry Augustus Purdie as editor of their Bulletin. In 1883, Allen, along with William Brewster and Elliott Coues, created the American Ornithologists' Union. Allen, who was suffering ill health, was unable to attend their inaugural meeting, but was elected their first president, nonetheless. He also became the chief editor of their journal, The Auk. In 1885, he was appointed as the first curator of birds and mammals at the American Museum of Natural History in New York, later becoming the first head of the museum's Department of Ornithology. In 1886, he was one of the incorporators of the first Audubon Society, New York City. He was a member of the American Association for the Advancement of Science, and of the American Philosophical Society. The hundreds of letters which Elliott Coues sent to him over many decades form one of the cornerstones of the history of American ornithology. Allen famously memorialized Coues in the pages of The Auk, the union's journal, after the latter's death in 1899. He formulated what is now known as Allen's rule, stating a correlation between body shape and climate, in 1877.
