Although the search for the drivers of amphibian declines continues, there is a need to implement conservation actions. Conservation science usually does not deliver clear answers about which conservation actions are most effective and which ones should be implemented. Furthermore, results often cannot be used directly by conservationists. Given that resources are limited, there is a need to know which conservation actions and management interventions are most likely to succeed. The goal of evidence-based conservation is to assess the effectiveness of conservation actions qualitatively and quantitatively, and comparative effectiveness studies are a powerful tool to evaluate different conservation actions. We use a case study on toad tunnels to discuss the benefits and limitations of comparative effectiveness studies. Although we show that wider tunnels are used by a higher proportion of individuals, the strength of evidence for effects of other characteristics of amphibian tunnels on tunnel use was weak. Despite some equivocal results, our case study illustrates that the approach can readily be used to study the effectiveness of conservation actions and to derive recommendations for conservationists and managers that can be used directly to improve future conservation interventions.