Integrating nature conservation effectively in forests managed for timber production implies reconciling a trade-off between ecological and economic objectives. In continuous cover forest management, this culminates in decisions about tree harvesting (or retention) determining both the prevalence of tree-related microhabitats in the forest and the economic viability of timber management. Applying an innovative mixed methods approach, we compare conservationists and foresters performing a tree selection exercise. We assess the outcomes of their forest management decisions quantitatively and explore their strategies and the underlying reasoning based on qualitative data. Our findings show that particularly the habitat trees differ greatly between the two groups: while conservationists retained almost exclusively large oaks at often high opportunity costs, foresters retained a notable number of smaller-diameter hornbeams. These differences are related to a different perception of opportunity costs of retention by both groups, as well as because they do not agree about how to value current tree-related microhabitats and their projection into the future. Such diverging patterns of reasoning imply incompatible interpretations of what constitutes a habitat tree. Our results indicate that it is important to apply benchmarks for evaluating ecological goals as well as to increase foresters’ and conservationists’ understanding about the motivations and restrictions of the respective counterpart. Our study points out a significant potential for (mutual) learning, and illustrates the complementarity of quantitative and qualitative research methods to examine tree selection behaviour.