Serhat Karakayalı received his PhD from Johann-Wolfgang-Goethe University in Frankfurt am Main and wrote his dissertation on the genealogy of illegal migration in Germany. At the same time, he co-designed and implemented the TRANSIT Migration project at the Institute for European Ethnology (Frankfurt). In this interdisciplinary research group, the concept of migration regime was linked back to empirical research, resulting in methods such as "ethnographic regime analysis", mediation tools and also a new network for critical migration research. In the meantime, he was, among other things, head of a project on anti-Semitism in the immigration society in Berlin and curator of an exhibition on modern architecture in the colonial context of North Africa.

From 2009, he worked as a post-doctoral researcher in the Department of General Sociology at Martin Luther University Halle-Wittenberg. From 2014, he was involved as a post-doc in the establishment of the newly founded Berlin Institute for Empirical Integration and Migration Research. His research focused on voluntary engagement with refugees, cosmopolitan concepts of solidarity, and civil society as a site of political socialization in the migration society. 

In 2016, he led the first representative survey to determine the proportion of members with a migration background in a large civil society organization – the metalworker’s union IG Metall, with over 2 million members. Following the findings of this project, he conducted a study on the motives and trajectories of migrant involvement in workplace co-determination, which was funded by the Hans Böckler Foundation. In the BMBF-funded collaborative project entitled "ZoMiDi," he worked with colleagues from Ludwig Maximilian University in Munich and the Max Planck Institute in Göttingen to examine how various civil society organizations deal with migration-related diversity in their structures. At BIM, he also led the Einstein Research Group on "Migration and Diaspora" and established the MERGE network.

From 2020, he was head of the "Migration" department at the German Center for Integration and Migration Research, a research institution funded by the German government, where he conducted research on migration in and from the Middle East as well as a series of public events, including on the crisis of refugee protection in Europe. The DeZIM Institute is also home to the Racism Monitor, commissioned by the German government, where Prof. Karakayali continues to be responsible for networking with international research and theoretical foundations. Since July 2021, he has been Professor of Migration and Mobility Studies at the School of Cultural Studies at Leuphana University.