Nature-based solutions (NbS), including green social prescribing (GSP), are sustainable ways to address health and wellbeing, especially since the COVID-19 pandemic exacerbated the strain on healthcare. NbS require national and local cross-sector coordination across complex, interrelated systems, but little is known about the specific challenges this poses for community-led NbS. We carried out a traditional literature review to establish the context and knowledge base for this study and interviewed 26 stakeholders. These came from environment, health and social care sectors at national and local levels, with local-level stakeholders from Bradford and Walsall: English cities significantly affected by the pandemic, with high levels of deprivation and health inequality. The interviews explored experiences of implementing NbS, both pre- and post-pandemic and the resulting renewed interest in the salutogenic effects of engaging with natural environments. We coded the interview transcriptions using NVivo to identify the challenges existing in the systems within which these stakeholders operate to create and manage NbS. By synthesizing what is known about the challenges from existing literature with findings from the interviews, we developed eight categories of challenges (perception and knowledge, political, financial, access to natural spaces, engagement, institutional and organisational, coordination, GSP referral and services) faced by multiple sectors in implementing community-led NbS in England. Furthermore, this study highlights the new challenges related to the pandemic. Identifying these challenges helps stakeholders in existing complex systems recognise what is needed to support and mainstream NbS in England.