Fossil embryos are paramount for our understanding of the development of extinct species. However, although thousands of fossil amniote eggs are known, very few embryos in ovo have been described. First reports of fossil embryos were based on broken eggs, where the embryonic remains were already exposed, because destructive methods on complete eggs were avoided. Investigations of complete eggs therefore required nondestructive approaches, such as X-ray microtomography (μCT). However, due to the general low density contrast between fossilized bones and infilling matrix, only a few specimens have been reported using these techniques. Using propagation phase contrast X-ray synchrotron microtomography (PPC-SR-μCT), we report here the discovery of three well-preserved embryos in Early Cretaceous eggs from Thailand. By scanning these eggs using different imaging techniques, we show that vastly different interpretations can be made regarding the preservation state and/or the developmental stage of these embryos. PPC-SR-μCT also revealed differential contrast between bone categories, presumably reflecting the ossification pattern of these embryos. Applying such an approach to large-scale studies of fossil eggs could lead to more discoveries and detailed studies of fossil embryos, providing important developmental and phylogenetic information on extinct and extant amniotes.