[2] 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.

[2] 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.

[3] For the next few years, Allen ventured to the Great Plains, Rocky Mountains, and Dakota Territory on collecting trips for Harvard's museum.

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.

Allen, who was suffering ill health, was unable to attend their inaugural meeting, but was elected their first president, nonetheless.