In 1964 Sekeris accompanied Karlson when he moved to the position of Director of the Institut für Physiologische Chemie of the Philipps University of Marburg. In 1966 he became a Privatdozent at the Medical School where, in 1970, he was promoted to “Wissenschaftlicher Rat und Professor”, and then to a C3 Professor. In 1974 he moved to the German Cancer Research Centre (Deutsches Krebsforschungszentrum) in Heidelberg as the Head of the Section “Molecular Biology of the Cell” and a professor at the Science Faculty of Heidelberg University. In 1977, he finally moved home to Greece as a Professor of Biochemistry at the University of Athens, first at the Department of Biology and then (1993) at the Medical School. During his tenure at the University of Athens he held a joint appointment at the Institute of Biological Research at the National Hellenic Research Foundation, serving as its Director. In 2000, he reached the mandatory retirement age for the Greek Public Service, but kept performing research, unofficially, up until his death in 2009. 
Sekeris’ main research interest was the mode of action of steroid hormones. He started his research working on tyrosine metabolism in insects and then rapidly moved to molecular endocrinology, where he stayed. Building on the work of Adolf_Butenandt (Karlsons father-in-law and director of the Munich Institute), Karlson and Sekeris early on proposed a model on how steroids function, which was very loosely based on Jacob and Monods model for the regulation of the lactose operon of Escherichia coli. He concentrated his later work on steroid receptor(s) including the binding of glucocorticoid receptor to mitochondrial DNA, which he and his group first described. His overall focus could be described as the elucidation of the role of glucocorticoids in the regulation of gene expression and cellular metabolism. This research led to research on post-transcriptional events such as mRNA processing. He was the first to describe the presence of small RNA species involved in the processing of hnRNA. He published more than 250 papers  and book chapters, making him one of Greece's most prolific scientists in non-clinical life sciences.
In addition to his long-term directorship of the Institute of Biological Research at the National Hellenic Research Foundation, Sekeris was involved in science administration both in Greece and abroad. He was a member of the Greek Research Council and acted as the Chief Executive Officer of the National Hellenic Research Foundation. Among different honours that he received during his career one should mention his election to the European Molecular Biology Organization (EMBO) and the European Academy of Sciences. After leaving Germany he was made an Honorary Professor of Cell Biology at the Science Faculty of Heidelberg University.