In the winter of 1841–1842, he joined John Lloyd Stephens and Frederick Catherwood on their expedition to Yucatán, where he created a sensation in the town of Mérida by performing eye surgery on several inhabitants who were afflicted with strabismus.

[5] He collected a large number of birds in Yucatan during the Stephens expedition in 1841–1842, and over the next decade he published notes and descriptions of many of them, including at least a dozen that were new to science.

[2][6] In the 1850s the obligations of his medical work forced him to give up publishing on ornithological topics, but he retained a strong interest in the subject until the end of his life.

[5][6] William Brewster praised his "remarkably keen and analytical mind," and believed that, had he continued in the field, "he would, without question, have become one of the most eminent of the ornithologists of his time.

Cabot was an abolitionist who served as secretary for the New England Emigrant Aid Company, which worked to stop the spread of slavery by sending anti-slavery settlers to the Kansas Territory in the wake of the Kansas–Nebraska Act of 1854.