Norway spruce (Picea abies) is an economically significant tree species native to northern and central Europe. Somatic embryogenesis (SE) presents an in vitro strategy for clonal propagation of tree species that are difficult to propagate vegetatively using cuttings. Deployment of the SE process for industrial scale production of Norway spruce plants is however hindered by embryogenic cell lines with different degrees of success in embryo development. To better understand the differences in embryo development among cell lines, we analyzed the metabolic profiles of cell lines with normal, aberrant and blocked embryo development. Using manual time lapse photography we followed embryo development from pro embryogenic masses (PEMs) to mature embryos in each of the three cell line. Metabolite profiles for each cell line during the course of somatic embryo development were compiled using Gas Chromatography coupled with Mass Spectrometry (GC/MS). Key metabolites were identified for each developmental stage in all cell lines using Multivariate statistical analysis tools. Potential candidate metabolites significant for normal embryo development were identified.