To illustrate the importance of theories-of-change (ToCs) for evaluation of conservation interventions, we consider the global ToC from the Forest Stewardship Council (FSC) and then develop a more explicit ToC focused on the sustained timber yield (STY) aspiration for natural forest management in Indonesia. We use these ToCs to consider certification implementation processes vis-à-vis indicators for STY extracted from FSC’s Indonesian Stewardship Standard that mentions STY explicitly in 45 and implicitly in 21 of 237 indicators. Analysis of 38 audit reports about 23 enterprises (2001–2017) revealed that only 77 of 504 major non-conformities assigned by auditors addressed STY. This apparent lack of attention to STY is surprising given the exhaustion of timber stocks in many production forests and the closure of many forest enterprises over the past two decades, but our ToC reveals numerous unsatisfied and unsatisfiable assumptions in certification that preclude detection of unsustainable harvests. Furthermore, compliance with governmental regulations on harvest intensities does not allow full timber recovery. To sustain yields, logging intensities need to be reduced and/or silvicultural treatments applied to increase yields, both of which reduce short-term profits. Declining yields might be accepted if the capacity of logged forests to grow timber is not impaired, but forest abandonment due to timber stock depletion is worrisome if it fosters illegal forest conversion.