First opened in 1955 as the mission to West Germany, it is currently located in the Mitte locality of central Berlin, just beyond the periphery of the Reichstag complex and near the Charité.

[2] Formal diplomatic relations between the Philippines and West Germany were established on October 8, 1954,[3] and after the two countries signed a trade agreement on April 25, 1955,[4] a legation in Bonn was opened that year,[2] with Jose D. Ingles becoming the mission's first resident envoy.

[2] The former embassy continued to serve as an extension office until it was closed in 2008 as part of a rationalization program and replaced the following year with the opening of the Philippine Consulate General in Frankfurt.

[15] That chancery, located on the building's sixth floor, had a 300 m2 (3,200 sq ft) reception area and a grand piano that was used for improvised concerts.

Cleofe Natividad, then began searching for a new property,[20] with the process formally kicking off on May 11, 2012 alongside procurement for the construction of a new chancery for the Philippine Embassy in Islamabad.

[21] Negotiations opened in late 2013 for the construction of a chancery on Von-der-Heydt-Straße in Berlin's diplomatic quarter, south of the Tiergarten, with Düsseldorf-based HPP Architekten serving as consultant to the project.

[23] Despite those agreements being signed, the project was likewise not able to proceed due to several factors, including a lack of funds, the hot Berlin real estate market and the slow pace of bureaucracy, which ultimately led to the construction of the present-day chancery.

[24] In the 19th century, the site was once home to Robert Leyser, a Jewish tailor and an ancestor of noted trade unionist Ludwig Rosenberg.

[27] Construction of the building was complicated by the street corner's slope, and also had to factor in urban design and historical preservation considerations due to its proximity to the Charité and the aesthetics of the surrounding neighborhood.

[24] The Philippine Embassy in Berlin is currently headed by Ambassador Irene Susan B. Natividad, who was appointed to the position by President Bongbong Marcos on November 22, 2022.