FDC began in 1968 as the Research Department of the Food Terminal Incorporated (FTI) known at that time, as the Greater Manila Terminal Food Market. Its task was to develop grade standards for fresh produce.

From 1969 to 1979, as FTI grew into a food storage and marketing center, FDC became involved in freezing, packing, and food storage activities. This gave FDC experience in food processing and low-temperature storage at a commercial level.

From 1980 to 1985, FTI as part of the National Food Authority (NFA), operated a chain of food stores known as the KADIWA Centers. In this program, FDC had to ensure the quality of almost 500 million pesos worth of fresh and processed foods sold nationwide at the “Kadiwa Centers” and exported to the United States and other foreign markets. This gave FDC experience in food quality control at a commercial level.

In 1986, when the Kadiwa Centers were dissolved, FDC offered its vast experience in evaluating and preserving food quality to the food export industry as a Food Development Center. At the same time, FDC became the implementing arm of NFA under a Memorandum of Agreement for technical exchange and product certification with the United States Food and Drug Administration.

In March 1987, FDC was transferred to the National Food Authority as one of its directorates. This was required by two foreign commitments of government, namely: a) an NFA loan from the Asian Development Bank, for an Agro-Processing and Marketing Project which funded the upgrading of FDC’s facilities in 1982, and b) an agreement between the Japanese and the Philippine governments in 1986 and formalized in October 1987 for the building of the Food Development Center Project as a donation from Japan.

In March 1989, FDC transferred to the two billion and forty-seven million yen (¥2,047,000,000.00) R&D facility donated by the Japanese government. Since then it has expanded its programs of technical assistance to the food industry.

In February 2004, FDC obtained ISO 9001:2000certifications for its quality management system for design, development, and provision of appropriate technologies, training, product and process evaluation, certification, and standards development. FDC obtained its certification to ISO 9001:2008 in May 2010 and in September 2018 to ISO 9001:2015 upon passing the transition audit conducted by the certification body.

In February 2015, FDC obtained ISO/IEC 17025:2005 accreditation for its Chemical and Microbiological Laboratories from the Philippine Accreditation Bureau of the Department of Trade and Industry. FDC obtained its certification to ISO/IEC 17025:2017 in October 2018.

In 2020, FDC was transferred to the Department of Agriculture through the enactment of the Republic Act (RA) 11203 “ An Act Liberating the Importation, Exportation, and Trading of rice, Lifting for the Purpose the Quarantine Import Restriction on Rice, and for Other Purposes.” Specifically, Rule 3.4.2 states that” The Department of Agriculture (DA) and NFA shall formulate the guidelines and organizational modification plan on the transfer of the Food Development Center (FDC) from NFA to the DA within (15) days upon the effectivity of the IRR for submission to the Department of Budget and Management (DBM). The FDC is the department of NFA in charge of providing scientific support on food safety, particularly on testing, research, and training…”