While at the Smithsonian Astrophysical Observatory (SAO), Abbot would work under Samuel P. Langley. Langley would go on to change his focus from solar radiation to aeronautics, with Abbot taking over solar radiation research. Abbot would participate in many expeditions. In 1900 he, along with Langley, would travel to Wadesboro, North Carolina to observe a solar eclipse, followed by another eclipse expedition to Sumatra in 1901. During his expedition experiences he would also travel to Algeria, Egypt, South Africa, Australia, and other countries, often in partnership with the National Geographic Society. Abbot would become acting Director of SAO in 1906 and in 1907, Abbot became the Director of the Smithsonian Astrophysical Observatory, following the death of Samuel P. Langley. While Langley was still Director, he had visited Mount Whitney, and decided it would be a great place for an observatory. Abbot secured funding for the observatory and it was built in 1909. As Director, a position he would hold until his retirement, Abbot would open the Radiation Biology Laboratory in 1929, to study radiation effects on plants, and other organisms. This helped to develop the first wave of biophysics researchers in the United States.