Over the past decades, science funding shows a shift from recurrent block funding towards project funding mechanisms. However, our knowledge of how project funding arrangements influence the organizational and epistemic properties of research is limited. To study this relation, a bridge between science policy studies and science studies is necessary. Recent studies have analyzed the relation between the affordances and constraints of project grants and the epistemic properties of research. However, the potentially very different affordances and constraints of funding arrangements such as awards, prizes and fellowships, have not yet been taken into account. Drawing on eight case studies of funding arrangements in high performing Dutch research groups, this study compares the institutional affordances and constraints of prizes with those of project grants and their effects on organizational and epistemic properties of research. We argue that the prize case studies diverge from project-funded research in three ways: 1) a more flexible use, and adaptation of use, of funds during the research process compared to project grants; 2) investments in the larger organization which have effects beyond the research project itself; and 3), closely related, greater deviation from epistemic and organizational standards. The increasing dominance of project funding arrangements in Western science systems is therefore argued to be problematic in light of epistemic and organizational innovation. Funding arrangements that offer funding without scholars having to submit a project-proposal remain crucial to support researchers and research groups to deviate from epistemic and organizational standards.