Differentiation into diverse cell lineages requires orchestration of gene regulatory networks guiding diverse cell fate choices. Utilizing human pluripotent stem cells, we measured expression dynamics of 17,718 genes from 43,168 cells across five time points during cardiac-directed differentiation. We used unsupervised clustering to identify the transcriptional phenotype of 15 subpopulations correlating with germ layer and cardiovascular differentiation in vivo. These data reveal transcriptional networks underlying lineage derivation of mesoderm, definitive endoderm, vascular endothelium, cardiac precursors, and definitive cardiac fates including contractile cardiomyocytes and non-contractile derivatives. Utilizing a customized lineage trajectory prediction algorithm, scdiff, we analyzed transcription factor regulatory networks as a basis to link subpopulations from time course single cell data to predict fate choices from pluripotency into the cardiac lineage. While contractile cardiomyocytes follow a trajectory of known gene regulatory networks, we identified PBX1, a transcription factor involved in outflow tract (OFT) development, as a regulator of non-contractile cardiac derivatives. This phenotype was confirmed by Spearman rank correlations comparing in vitro-derived OFT cells against single cell isolated subpopulations of the E9.5 mouse heart. We identified the non-DNA binding homeodomain protein, HOPX, as a candidate regulator underlying cardiomyocyte vs OFT fates in vitro and in vivo. While HOPX is one of the earliest functional regulators of cardiac fate in vivo, we show that HOPX is expressed late and in only 16% of cardiomyocytes and has a repressive chromatin state during in vitro differentiation. Using genetic loss of function hiPSCs coupled with physiological assessment of engineered heart tissues, our findings implicate dysregulation of HOPX during in vitro cardiac-directed differentiation underlying the molecular and physiological immaturity of stem cell-derived cardiomyocytes. Overall, this study provides the first single cell decomposition of cardiac directed differentiation providing a basis for dissecting in vitro cell fates for developmental studies and disease modelling.