Utrecht University and the Netherlands Foundation for Chemical Research (SON) founded the Bijvoet Center for Biomolecular Research as a joint research institute on March 25, 1988. The objective of this collaboration was to create a center for research and expertise in structural biology with an internationally recognized academic staff and an advanced instrumental and computational infrastructure. The identification of a steadily increasing number of genome sequences has generated a need for functional studies to elucidate the molecular mechanisms of life. Originally, the institute consisted of four groups focussing on different aspects of biomolecular research: NMR Spectroscopy, Crystal- and Structural Chemistry, Biomembranes and Modelsystems and Bio-organic Chemistry of Glycoconjugates. Since that time, the institute has evolved and diversified and, as of 2019, consist of seven core research groups at Utrecht University, and additional associated groups at Utrecht University and the University Medical Center Utrecht (UMCU).

Nowadays, the Netherlands Foundation for Chemical Research is part of the Netherlands Organization for Scientific Research (NWO), which promotes scientific research at Dutch universities, in part by supporting national research institutes and facilities. Since its estalishment, the Bijvoet Center has received significant support for its research programmes and research infrastructures from NWO, the European Union, Utrecht University, and many other companies and organizations. 

Since its start, the Bijvoet Center has provided educational programs for young researchers to prepare them to meet the challenges of future life science research. It always has hosted a large number of both Dutch and international PhD, master and bachelor level students with backgrounds in Chemistry, Pharmacy, Biology, Biomedical Sciences and related fields. Between 1992 and 2014, the PhD educational programme of the Bijvoet Center for Biomolecular Research was formally accredited by the Royal Netherlands Academy of Arts and Sciences (KNAW). Since 2015, the educational programme is assessed every six years using the Standard Evaluation Protocol developed by the Association of Universities in the Netherlands (VSNU).