We here report a flow-cytometry-based protocol to measure single-cell protein expression in small samples. The protocol is optimized for simultaneous detection of fluorescent proteins and intracellular and surface antigens in the embryonic pancreas from the mouse. Owing to low cell numbers, current protocols for flow cytometric analysis of embryonic tissues rely on tissue pooling. Our protocol enables analysis of one pancreas per sample, thereby facilitating detection of biological variation and minimizing the number of experimental animals needed. For complete details on the use and execution of this protocol, please refer to Nyeng et al (2019).