Following her work at Tenampúa, Popenoe ranged widely in Honduran archaeology. In 1927, she began work at the hilltop site of Cerro Palenque on the Ulua River. Unfortunately, her field notes were lost, and she produced no report, although photographs in the Peabody Museum document the area of the site at which she worked. According to doris stone, a contemporary who also worked in Honduras, Popenoe believed Cerro Palenque was a sixteenth-century fortress related to Tenampúa. An unpublished typescript on copper bells in the collections of the Tozzer Library at Harvard University may relate to otherwise undocumented work at La Majada caves in the Department of Santa Barbara, suggested by the donation to the Peabody Museum of bells with this provenience in 1930.

A report in 1910 by A. H. Blackiston had described a metal cache from a cave in the same region as probably the goods of a wandering Mexican Toltec trader and smith. It is likely that Popenoe was familiar with this report, as she cited another paper by Blackiston in the same journal. This paper had described burials eroding into the river at a site Blackiston called Playa de los Muertos, or “beaches of the dead.” Popenoe chose the same name for the site of the burial excavations that initiated her collaboration with the Peabody Museum. She identified it as one of the locations explored in the 1890s by G.B. Gordon for the Peabody Museum, documenting her familiarity with his report as well.

Popenoe’s published account of her excavations at Playa de los Muertos says that she broke off work at Cerro Palenque when reports of burials washing into the Ulua River a few miles downriver reached her in 1928. Her salvage of burials that season sparked her interest in the site, to which she returned the following year. By then she had made contact with Alfred M. Tozzer of the Peabody Museum, to whom she looked for guidance in her subsequent work. Although documentation for her initial introduction to Tozzer is lacking, later correspondence suggests that Thomas Barbour, who was a naturalist at the Museum of Comparative Zoology at Harvard and a member of the Peabody Museum’s governing board, may have put Popenoe in contact with his archaeological colleague.

Tozzer supported the continuation of Popenoe’s research in Honduras beginning with her second season of work at Playa de los Muertos. Correspondence relating to the collections from this site in the Peabody Museum shows that he encouraged her to use the work as an opportunity to clarify the relative chronological placement of monochrome and polychrome pottery in Honduras. The existence of two separate pottery complexes in the Ulua Valley had been established by G. B. Gordon, who felt they represented two separate cultures. Tozzer, who supervised George Vaillant’s seriation of Mayan pottery, including the Ulua polychromes, believed the pottery types represented distinct time periods and urged Popenoe to seek burials, the contexts he believed best suited to establish chronological relationships, containing monochrome and polychrome pottery.

Popenoe exposed a series of burials at Playa de los Muertos now known to date to the middle formative period, preceding the Ulua polychromes of the classic period. Because she did not also find polychrome burials there, Popenoe continued to search for other sites with both ceramic complexes. Her excavations in 1930 and 1931 at Siguatepeque and along the Ulua River, described in manuscripts at the Peabody Museum and represented by collections deposited there, produced evidence of stratigraphic superposition. She describes her approach to these excavations as “the horizontal,” or “onion-peel” method, resulting in identification of surfaces with dispersed remains of single vessels. She correctly interpreted the stratigraphy she isolated and related it to her results from Playa de los Muertos.

It was at this juncture that she unexpectedly died in 1932. Accounts of the cause of death cite accidental ingestion of poisonous akee, planted at the Lancetilla station. After her death, Tozzer prepared her Playa de los Muertos report for publication, framing it with a paper by George C. Vaillant that used the data from Playa de los Muertos to address the wider question of the origins of formative period culture. Although the Playa de los Muertos report is thus usually cited as the basis for the definition of the so-called