The past three decades have witnessed a sharp reduction in the rate of growth of public research funding, and sometimes an actual decline in its level. In many countries, this decline has been accompanied by substantial changes in the ways that such funding has been allocated and monitored. In addition, the institutions governing how research is directed and conducted underwent significant reforms. In this paper we examine how these changes have affected scientists’ research goals and practices by comparing the development of three scientific innovations (one each in physics, biology, and educational research) in four European countries, namely Germany, the Netherlands, Switzerland, and Sweden. We find that the increased number of actors exercising authority over research goals does not necessarily lead to a greater diversity of interests funding research. A narrowing of goals and frameworks is especially probable when the increasing importance of external project funding is combined with reductions in state financing of universities and public research institutes. Finally, the growing standardisation of project cycle times and resource packages across funding agencies and scientific communities make it more difficult for researchers to pursue projects that deviate from these norms, especially, if they challenge mainstream beliefs and assessment criteria.