The establishment of a Philippine diplomatic presence in the then-Federation of Malaya was first called for in the second State of the Nation Address of President Carlos P. Garcia,[1] which led to the opening of a legation later that year shortly after the country attained independence.

[5] Five years later, President Ferdinand Marcos ordered the Embassy to close again after Senator Benigno Aquino Jr. exposed the Jabidah massacre, leading to Malaysia breaking off all diplomatic relations with the Philippines.

[11] The 2012 renovation, the most extensive of the three, entailed converting the building from its previous residential layout, which was said to look "undistinguished",[10] to an open floor plan more suited to the office functions of an embassy, while still retaining the exterior of the historically significant property.

[11] Led by then Ambassador J. Eduardo Malaya and Malaysia-based Filipino architect Bart Vista, the renovation, which began in February 2012, included converting and expanding the former dining room into a new community hall, extensively replacing flooring and other features, updating the building's electric wiring and air conditioning systems, installing new stained glass and lighting fixtures, repainting the building's exterior, and redoing the compound's landscaping.

34 dated 25 January 2017, commended Ambassador Malaya for his “proactive leadership” and Architect Bart Vista for his exemplary kindness and patriotism in relation to the renovation project.

In 2016, Ambassador Jose Eduardo Malaya III and two other embassy officials were awarded the Gawad Mabini for setting up alternative learning centers for Filipinos and other migrant children in Sabah.