This case study aimed to assess the potential threats to the Linnaeus botanical heritage in Uppsala Municipality, focusing on the Linnaeus Trails and their surroundings. These trails are part of Uppsala's green infrastructure, providing cultural and supporting ecosystem services that enhance urban resilience.  The study investigated potential threats to the Linnaeus trails from different angles, including management and governance, urban expansion, habitat fragmentation, wear and tear, UNESCO World Heritage plans, genetic contamination, and invasive species. Data was collected through reviews of scientific literature and municipal governance documents, with informants providing additional insights, clarifications, and primary data. The authors also compared historical and current maps to identify changes over time and conducted study visits to verify the information. The findings revealed that the Linnaeus botanical heritage is threatened in all examined areas, with urban expansion, landownership issues, habitat fragmentation, and genetic contamination identified as the primary threats. Additionally, shifting baselines and landownership were highlighted as significant concerns. The findings also showed that the botanical heritage and the Linnaeus Trails are most protected within designated nature reserves. However, the management of the Linnaeus heritage involves numerous stakeholders, which might lead to instability in preservation strategies.  To address these challenges, the authors propose that the municipality should establish a biological rescue plan for the Linnaeus botanical heritage, complementing Uppsala’s Green Plan. This plan should guide stakeholders in avoiding genetic contamination and utilise expertise from SLU and Uppsala University to protect Linnaean species. A centralised governing body should be responsible for the long-term management. Allocating more resources for communication and advocacy around the Linnaeus Trails will help garner public and political support. Awareness of shifting baselines in urban planning is essential for protecting this heritage. In conclusion, this case study underscores the need for coordinated and proactive measures to protect the Linnaeus botanical heritage from environmental and anthropogenic threats.