Ancient organic remains are essential for the reconstruction of past human lifeways and environments but are only preserved under particular conditions. Recent findings indicate that such conditions are becoming rarer and that archaeological sites with previously good preservation, are deteriorating. To investigate this, we returned to the well-known Swedish Mesolithic site Ageröd I. Here we present the result of the re-excavation and the osteological analyses of the bone remains from the 1940s, 1970s and 2019 excavation campaigns of the site, to document and quantify changes in bone preservation and relate them to variations in soil conditions and on-site topography. The results indicate that the bone material has suffered from accelerated deterioration during the last 75 years. This has led to heavily degraded remains in some areas and complete destruction in others. We conclude that while Ageröd can still be considered an important site, it has lost much of the properties that made it unique. If no actions are taken to secure its future preservation, the site will soon lose the organic remains that before modern encroachment and climate change had been preserved for 9000 years. Finally, because Ageröd has not been subjected to more or heavier encroachment than most other archaeological sites, our results also raise questions of the state of organic preservation in other areas and call for a broad examination of our most vulnerable hidden archaeological remains.