Using advances in stratigraphy building on the work of Flinders Petrie, they developed a chronology for the region using ceramic typology.

Upon Bliss' retirement, Macalister became director of excavations for the Palestine Exploration Fund (PEF) in 1901.

Macalister also documents his findings of child sacrifices around the High Place of Gezer, by the Amorites, a tribe of Canaan.

During this period, he worked at the ancient Irish royal site at the Hill of Tara and was responsible for editing the catalogue of all known ogham inscriptions from Great Britain and Ireland.

He is buried at the Parish of the Ascension Burial Ground in Cambridge, with his wife Margaret A. M. Macalister.