The adoption of the UN Statistical Standard for Ecosystem Accounting (SEEA-EA) has reignited interest in developing a coherent natural capital framework for urban environments among scholars and policymakers. As the EU Nature Restoration Law indicates, it is urgent to transition towards a pathway of continuous, long-term, and sustained recovery of biodiversity. To elaborate a system of standardised ecosystem accounts would help (i) monitoring continuously the state of natural and anthropogenic ecosystems, and (ii) tracking progress of ecosystem restoration targets. However, scholars have realised that SEEA-EA still does not offer a rigorous ecological conceptualisation for urban ecosystems and that the lack of a fit to purpose operational framework might hamper its practical implementation in EU cities. Here, we review current ecosystem accounting theory and practice with the aim of highlighting critical conceptual and operational challenges of SEEA-EA for urban ecosystem accounting. For some challenges, potential solutions are also discussed. We explored core grey and white literature on SEEA-EA and conducted our review using both traditional systematic and a cutting-edge review tool, which prevented overlooking relevant references not making use of SEEA-EA terminology. To complement, and double-check findings, insights from experts on challenges and potential solutions were also gathered. Our results highlight a greater number of conceptual challenges in extent and condition accounts. Among those, it emerges a lack of consensus on where and how to delineate the boundaries of urban ecosystems. Moreover, the definition of sub-functional groups of urban ecosystems reveals to be still in its infancy. We also identified challenges shared with other ecosystems (like wetlands or agroecosystems), thus making our findings relevant beyond urban accounting. By visibilizing challenges and discussing feasible solutions from an ecology lens, we expect to help building the basis of a coherent and ecologically robust system of SEEA-EA urban ecosystem accounts in EU.