Labelling and tracking cells in vivo is a powerful tool for studying development, allowing lineage tracing and fate mapping on a single-cell level. However, current methods for labelling post-implantation mouse embryos are technically challenging and/or of limited efficiency. In this Techniques and Resources paper, Miguel Torres and colleagues develop a novel method for single-cell tracing and manipulation using a cell-permeant Cre recombinase (TAT-Cre) system. Here, the authors microinject the TAT-Cre protein to permanently activate fluorescent reporters, allowing single-cell labelling and subsequent clonal analysis of cell progenitors in the nascent mesoderm. The authors also build on this technique to perform localised knockdown of Mycn, a gene essential for maintaining cell proliferation in embryonic cardiomyocytes. Here, they demonstrate that Cre-mediated knockdown of Mycn recapitulates reduced proliferation of cardiomyocytes seen using genetic approaches, confirming the cell-autonomous role of Mycn here and also the specificity and effectiveness of this TAT-Cre method. In conclusion, this new single-cell labelling system offers a more accessible and precise method for single-cell labelling, genetic manipulation and clonal analysis in mouse embryos.