Unpicking cell or non-cell-autonomous gene functions can be difficult to achieve in vivo. Now, Alexandra Wehmeyer, Sebastian Arnold and colleagues demonstrate how chimeric gastruloids can be used to study the roles of Tbx transcription factors, eomesodermin (Eomes) and brachyury, during mammalian peri-gastrulation development. The authors combine fluorescently labelled wild-type embryonic stem cells (ESCs) with genetically modified gain- or loss-of-function ESCs by merging aggregates formed from both populations or mixing the two cell types. Using the merging approach, the researchers show that Eomes-expressing cells autonomously organise and instruct the formation of a cardiogenic domain, as shown by the emergence of beating tissue and the expression of cardiac markers. In chimeras formed from the mixing of wild-type and brachyury mutant (Bra-/-) cells, they show that axis elongation is disturbed by a high contribution of Bra-/- cells. Bra-/- cells non-cell-autonomously reduce Bra expression in wild-type cells by reducing Wnt signalling activity. Furthermore, Bra-/-cells autonomously accumulate at the posterior pole and midline, and contribute to primitive gut-like and neural tube-like structures that express key marker genes. Together, these data demonstrate how chimeric gastruloids are a rapid and versatile tool for studying gastrulation-stage embryogenesis with increased experimental accessibility.