The investment of decision makers in research can increase the likelihood that relevant and timely practice-based research questions are asked and that these findings are readily taken up into policy and practice. While many positive benefits may be gained from this type of research, various challenges may also arise along the way. These include: unpredictable practice settings and a change in priorities or study focus over time; time and staff workload; decision maker research knowledge and experience; and balancing applied research with good scientific practice. In this paper, we discuss these challenges and offer recommendations for overcoming them.