A first intensive archaeological exploration of the site was conducted in 1902 by Leopoldo Batres, then General Inspector of Monuments for the Mexican government under Porfirio Diaz (Batres 1902).
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By the Late Classic (Monte Albán IIIB/IV, ca. AD 500-1000) the site's influence outside and inside the valley declined, and elites at several other centers, once part of the Monte Albán state, began to assert their autonomy, including sites such as Cuilapan and Zaachila in the Valle Grande and Lambityeco, Mitla, and El Palmillo in the eastern Tlacolula arm.
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Over the following eighteen years Caso and his colleagues Ignacio Bernal and Jorge Acosta excavated large sections within the monumental core of the site, and much of what is visible today in areas open to the public was reconstructed at that time.
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A recent project directed by Charles Spencer and Elsa Redmond of the American Museum of Natural History in New York has shown that rather than being abandoned the site actually grew significantly in population during the periods Monte Albán Early I and Late I (ca. 500-300 BC and 300-100 BC, respectively) and might have actively opposed incorporation into the increasingly powerful Monte Albán state (Spencer and Redmond 2001).
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He was a part of the Valley of Oaxaca Settlement Pattern Project which focused on the evolution of the Monte Albán state and shifts in settlement in the region over three millennia.