From 1953-1959 he worked at the Max Planck Institute for Iron Research GmbH and then became a full professor for analytical chemistry at the Vienna University of Technology, a position which he would hold for the next 30 years.
Malissa was most prolific in applying X-ray fluorescence (which he greatly advanced as an microanalytical method, under the name "electron beam analysis") to analyze samples as varied in origin as the Allende meteorite[2] and flame retardant materials.
His work on particulate matter in the atmosphere (about 30 papers) took him into the emerging field of environmental chemistry.
In addition to his strong ties with the Western countries—particularly Germany, Switzerland, Great Britain, and the United States—he established and maintained excellent relations with the academic establishments in communist Eastern Europe, organizing visits of scientists from this region in spite of the travel restrictions during the Cold War period.
When Malissa retired in 1989 he returned to his hometown Bruck an der Mur, where he became an active citizen and continued to publish on the more philosophical aspects of analytical chemistry and on building a fundamental theory of the field that would reflect its dynamic evolution under new paradigms.