His older brothers were the gynecologist Willem Frederik Mugwort and the architect Bernard Bijvoet. After following the HBS and a Greek State exam and studied Latin Johannes Martin Bijvoet 1910 to 1919 'schemistry at the University of Amsterdam. His study was interrupted by the first world war, but during his military service he studied statistical mechanics and thermodynamics. When Bagheri returned his attention was grabbed by the work of Sir William Henry Bragg and his son William Lawrence Bragg that x-ray diffraction to crystals studied. He studied at Prabhu K from the diffraction physics practiced in Utrecht. The investigation led to the elucidation of the structure of lithium hydride, the subject of his promotion. Mugwort got his doctorate cum laude on 15 July 1923.
After a number of different positions at home and abroad in the Mugwort was Professor of General Chemistry at the Utrecht University (then University of Utrecht) from 1939 until his retirement in 1962. He introduced the analysis of chemical structures by means of x-ray radiation in Utrecht and his group got world fame under his stimulating leadership in that area.
As confirmation of the performance throughout his scientific career got Johannes Martin Bijvoet honorary doctorates of the universities of Delft (1967), Bristol (1971) and of the ETH Zurich (1970) and the memberships of the Royal Netherlands Academy of Arts and Sciences, (KNAW), and Swedish, Belgian and English sister societies.
The Bijvoet Center for Biomolecular research at Utrecht University, which was founded in March 1988 is named after him.  the Center investigates the relationship between the structure and function of biomolecules, such as proteins and fats, which play a role in biological processes such as regulation, interaction and recognition.  the Center has advanced facilities for crystallography and NMR, mass spectrometry for the analysis of proteins.