To better manage our environment, systematic information is needed on the state of ecosystems and their interactions with society. Efforts have been undertaken to design monitoring and recording systems, notably the United Nations System of Environmental-Economic Accounting (SEEA). However, the diverse conceptualizations and applications on ecosystem accounting found the scientific literature have never been assessed in a systematic way. Here, a systematic literature review on ecosystem accounting, i.e. natural capital accounting approaches that focus on ecosystems, is conducted to detail the evolving trends in concepts, methodologies, and applications, and to identify main gaps and challenges for future work. Results yielded 378 scientific articles published between 1990 and 2021. This literature is diverse in terms of frameworks developed, ecosystems studied, valuation methods used, and accounts produced. Among the eleven ecosystem accounting frameworks identified, the SEEA is the most widely used. This literature is moving from focusing on conceptual elements towards addressing implementation issues. It is primarily conducted in European countries, on forest ecosystems, using biophysical methods and monetary valuation methods consistent with exchange values to produce accounts. The gaps that should be the focus of future work include the issue of implementation: methodologies (artificial Intelligence technologies and economic valuation), data, for instance making better use of remote sensing images, collaborations, and supporting the use of ecosystem accounts in decision-making.