Madagascar's notoriously high level of biodiversity is currently threaten by deforestation. Protected Areas (hereafter “PAs”) remain until now the central instrument to protect it whilst little is known about their environmental effectiveness in the country. With a matching approach in a quasi-natural experiment setting, we demonstrate for the entire island's rainforest that PAs' additionality has been limited from 2001 to 2012. PAs have made it possible for deforestation to be stabilized in a trend and has restricted the upsurge of deforestation resulting from the country's late political instability. Nonetheless, post-matching analyzes reveal that PAs have only contained some of the causes of deforestation. Effectively stopping the latter will require further ambitious policies to trigger the necessary agricultural transition for the country.