A crucial topic in Migration Studies is the exploration of refugees and other migrants’ mobility aspirations and behaviors over the life course. Beyond micro-trajectories and individual characteristics, a central role is played by the uncertainty connected to political, social and cultural contexts and to structural conditions both in native and host country. Using original data from the Refugee Sample of the German Socio-Economic Panel and performing logistic regression analyses, we investigate the intention to stay in Germany permanently, the intention to leave and the uncertainty about future mobility choices of 7,134 adult refugees arrived from Syria, Iraq, Afghanistan, Eritrea and Iran after 2011. For what concerns conditions in destination, in line with previous studies, we found that factors shaping onward migration or return intention are mainly related to labor market integration and mismatch with qualification and linguistic integration, along with family members’ place of residence. Nevertheless, the main contribution of this paper can be claimed for the relevant role played by soft indicators such as wellbeing measures, worries and concerns about the future, triggering uncertainty in refugees’ mobility choices linked to conditions in origin country, legal and policy evolution and public discourses about ethnic minorities in destination country.