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Forest certification, a proxy for sustainable forest management, covers more than 10% of the world's forests. Under forest certification, forest managers and landowners must comply with environmental, economic and social management standards aiming to promote forest conservation. Despite an increasing area of certified forests, there is a dearth of data on how forest certification is affecting the conservation of forest ecosystems and associated habitats. Here, we assess the effects of Forest Stewardship Council (FSC) certification, one of the largest certification schemes in the world, on the ecological condition of streams crossing Mediterranean evergreen oak woodlands. We used the Stream Visual Assessment Protocol (SVAP) to compare the ecological condition of streams located in areas with 3 and 5 years of certification, in non‐certified areas and in least disturbed streams. Forest certification positively affected the ecological condition of the surveyed streams, but its effects were only measurable after 5 years of certification. Streams with 5 years of certification had more continuous, dense and diverse riparian vegetation when compared to streams located in non‐certified areas. Moreover, the condition of streams located in areas with 5 years of forest certification was similar to the condition of least disturbed streams. Synthesis and applications. Forest certification promotes the ecological condition of streams occurring within Mediterranean evergreen oak woodlands. This mainly happens because in areas under forest certification, managers and landowners have to comply with management practices that require them to remove or reduce the main causes for stream degradation, allowing riparian habitats to recover. Within landscapes with large and increasing areas under forest certification, such as the Mediterranean cork oak woodlands, the positive effects of certification on the ecological condition of streams may spread across the hydrographic network in the medium to long term.