Human stem-cell-based embryo models (hSCBEMs) offer unprecedented opportunities for basic and translational research. However, the rapid pace of scientific developments in the field challenges the slower, traditional modes of ethics evaluation. To facilitate responsible research and governance, and ensure public trust, we propose using ‘embedded ethics’ as a purpose-anchored, dynamic, iterative and integrative approach where ethicists and scientists engage in continuous dialogue to ethically assess ongoing research. We outline a nested benchmarking strategy to periodically evaluate the scientific and ethical status of hSCBEMs within a project, using the human embryo as a reference and weighting criteria along a hierarchy of features that chart embryo-likeness, completeness and the developmental stage modelled. Embedded ethics guides the definition of decision points and ethical boundaries through an iterative assessment of project purpose and ethical and regulatory frameworks, and enables early identification of emerging issues and the co-construction of responsible paths forward.