In the newly created Department of Foreign Affairs that held offices first at Malacañang Annex then moved to Arlegui Street in Manila, Guerrero applied in August 1946 for a post and was accepted, becoming the assistant chief of division, Division of European and African Affairs under Dr Jacinto C. Borja. Under the Office of Political and Economic Affairs, the division was responsible for the crafting of governmental policy in its conduct of relations with states of Europe and Africa. As assistant chief, he assisted Borja in developing basic country and area studies to guide Philippine foreign policy in those countries. He consulted various offices and agencies of the government in the formulation of policy; provided information to these offices to guide them in the conduct of their activities that impinge on Philippine policy towards other countries, and other tasks. He also worked with Teodoro “Doring” Evangelista, still his superior, who held office at the Office of the Counsellor on Political and Cultural Affairs. The wartime ministry became the nucleus of the new department.

Guerrero was also taken in as confidential secretary to Vice President, and also Secretary of Foreign Affairs Elpidio Quirino. He wrote memos, letters, speeches and would perform other tasks ordered by Quirino such as taking down notes in meetings presided by his boss. Then, he was promoted to Chief of Protocol. By virtue of the reorganization implemented in January 1947, the Division of Protocol was placed under the office of Undersecretary Bernabe Africa. As head of the division, Guerrero was responsible for arranging the presentation of ambassadors and ministers accredited to the government. He corresponded with foreign governments on their acceptability and the acceptability to foreign governments of Filipino counterparts. He arranged national and international events here and abroad in which the Philippines participated; made arrangements for the visit of Philippine officials and organizations abroad; arranged for the entry of American forces and their supplies in accordance with treaties; prepared letters of credence, commissions, exequaturs, certificates of recognitions, and other correspondences regarding the exchange of diplomatic and consular representatives and the opening and closing of diplomatic and consular offices; and maintained a record of all officers and staff of foreign governments in the Philippines and published it into a list annually.