It became a visita of Marikina, and as popular folklore has it that a small chapel was built near a cross-shaped marking nut tree known in Tagalog as ligas stood.

[5] After the Battle of Pasong Tamo on 26 August 1896, during the Philippine Revolution against Spain, Andres Bonifacio, Emilio Jacinto, Guillermo Masangkay, Pio Valenzuela and other Katipuneros camped in Krus na Ligas and met in one of the houses fronting Plaza Santa Inez before heading to San Juan del Monte.

[4][6][7] In 1939, Krus na Ligas together with the barrios of Balara, Diliman, Barangka, and Jesus de la Peña were separated from Marikina to form part of Quezon City.

On April 2, 1949, a vast tract of public land which tilled by residents of the surrounding communities including Krus na Ligas was authorized by President Elpidio Quirino to be sold to the University of the Philippines for one peso, for it to build its new campus outside of Manila.

This resulted into several court cases attempting to secure legitimate ownership of the land the residents claim to have been in their family for generations, long before UP Diliman was even established.