"Intrinsic motivation crowding out", the erosion of high-quality, sustainable motivation through the introduction of financial incentives, is one of the most frequently discussed but yet little researched potential unfavorable consequence of Performance-based Financing (PBF). We used the opportunity of the introduction of PBF in Malawi to investigate whether and how PBF affected intrinsic motivation, using a mixed-methods research design theoretically grounded in Self-Determination Theory (SDT). The quantitative component served to estimate the impact of PBF on intrinsic motivation, relying on a controlled pre- and post-test design, with data collected from health workers in 23 intervention and 10 comparison facilities before (March/April 2013; n = 70) and approximately two years after (June/July 2015; n = 71) the start of the intervention. The qualitative component, relying on in-depth interviews with health workers in selected intervention facilities one (April 2014; n = 21) and two (September 2015; n = 20) years after the start of PBF, served to understand how PBF did or did not bring about change in intrinsic motivation. Specifically, it allowed us to examine how the various motivation-relevant elements and consequences of PBF impacted health workers' basic psychological needs for autonomy, competence, and relatedness, which SDT postulates as central to intrinsic motivation. Our results suggest that PBF did not affect health workers' overall intrinsic motivation levels, with the intervention having had both positive and negative effects on psychological needs satisfaction. To maximize positive PBF effects on intrinsic motivation, our results underline the potential value of explicit strategies to mitigate unintended negative impact of unavoidable design, implementation, and contextual challenges, for instance by building autonomy support activities into PBF designs.