Protected areas are a cornerstone for forest protection, but they are not always effective during times of socioeconomic and institutional crises. The Carpathian Mountains in Eastern Europe are an ecologically outstanding region, with widespread seminatural and old-growth forest. Since 1990, Carpathian countries (Czech Republic, Hungary, Poland, Romania, Slovakia, and Ukraine) have experienced economic hardship and institutional changes, including the breakdown of socialism, European Union accession, and a rapid expansion of protected areas. The question is how protected-area effectiveness has varied during these times across the Carpathians given these changes. We analyzed a satellite-based data set of forest disturbance (i.e., forest loss due to harvesting or natural disturbances) from 1985 to 2010 and used matching statistics and a fixed-effects estimator to quantify the effect of protection on forest disturbance. Protected areas in the Czech Republic, Slovakia, and the Ukraine had significantly less deforestation inside protected areas than outside in some periods; the likelihood of disturbance was reduced by 1–5%. The effectiveness of protection increased over time in these countries, whereas the opposite was true in Romania. Older protected areas were most effective in Romania and Hungary, but newer protected areas were more effective in Czech Republic, and Poland. Strict protection (International Union for Conservation of Nature [IUCN] protection category Ia-II) was not more effective than landscape-level protection (IUCN III-VI). We suggest that the strength of institutions, the differences in forest privatization, forest management, prior distribution of protected areas, and when countries joined the European Union may provide explanations for the strikingly heterogeneous effectiveness patterns among countries. Our results highlight how different the effects of protected areas can be at broad scales, indicating that the effectiveness of protected areas is transitory over time and space and suggesting that generalizations about the effectiveness of protected areas can be misleading.