Following the completion of his project in Athens, Haynes joined an American archaeological excursion to Assos, where he worked under Joseph Thatcher Clarke as an archeological photographer.

Despite being hired as a photographer for the project, Hayne's lack of equipment forced him to abandon photography during the 1881 dig season, and he instead became captivated by the archeological work.

Funded by the Archaeological Institute of America, Haynes and John Robert Sitlington Sterrett, who he had met during the expedition at Assos, spent the summer of 1884 documenting their travels through Anatolia.

He believed that many of the rock formations he photographed in Selime had been dwellings of early Christians fleeing persecution, and he planned on publishing a book on the matter, which never came to fruition.

Haynes photographs of this region were, however, published in a 1919 National Geographic article entitled "The Cone Dwellers of Asia Minor: A Primitive People Who Live in Nature-Made Apartment Houses Fashioned by Volcanic Violence and Trickling Streams".

[1] In 1887, Haynes set out on another expedition to Anatolia, funded by William R. Ware of Columbia University with the purpose of photographing archeological sites.

In October 1884, Haynes, together with his former partner John Sitlington Sterrett, William Hayes Ward, and Daniel Z. Noorian assembled in Mersin.

The first campaign ended in April 1889, mere months after the group arrived in Nippur, due to conflicts with local tribesman as well as clashes between Hilprecht and Peters.

In early 1899, Haynes returned to Nippur for one final season accompanied by his wife, Cassandra Artella Smith, and two young architects, Clarence S. Fisher and H. Valentine Geere.

[1] These tablets, along with other artifacts collected from the digs at Nippur, reside at the University of Pennsylvania Museum of Archaeology and Anthropology in Philadelphia and in Istanbul.