Global urbanisation has increased pressures on ecosystems located within city boundaries, resulting in loss and fragmentation of urban ecosystems. In September 2015, the United Nations adopted the 2030 Agenda for Sustainable Development which includes 17 Sustainable Development Goals (SDGs) and 169 SDG targets. It made environmental sustainability a key component of the agenda, whose preamble recognises that social and economic development depends on the sustainable management of Earth’s natural resources. Understanding the interlinkages between the broad and globally focused 2030 Agenda and components of the natural environment remain a practical challenge for both researchers and decision-makers in all disciplines. It is unclear how SDG targets relate to urban ecosystems and what evidence base supports these relationships. Here, we address what changes are required concerning urban ecosystem management and how management of urban ecosystems can reinforce or undermine action to deliver all 169 targets in the 2030 Agenda. We characterised 91 targets requiring action in relation to urban ecosystem management. These collectively emphasise the need to sustainably manage nature, provide equal rights to basic services, pursue sustainable economic growth, and strengthen governance and policy development at multiple scales. We identified 102 targets (99 synergies and 51 trade-offs) with published evidence of relationships with urban ecosystems, where decisions about urban ecosystems affect humanities ability to realise greater welfare and well-being, and build physical and social infrastructure. These findings highlight that sustainable management of urban ecosystems cannot be achieved without addressing other issues such as economic growth, equality or good governance. Translating these interlinkages into a strategy supported by all actors in society is important for achieving sustainable urban ecosystem management.