Astaxanthin (AX) is a carotenoid pigment with antioxidant properties. AX is used widely in the animal feed industry as a supplement. Wild-type strains of Phaffia rhodozyma naturally produce low AX yields, but we increased AX yields 50-fold in previous research using random mutagenesis of P. rhodozyma CBS6938 and fermentation optimisation. Genome sequencing linked phenotype and genome changes of the increased AX production but relevant metabolic changes were not resolved. In this study, the wild-type and the superior P. rhodozyma mutant strains were grown in chemically defined media and instrumented fermenters. Differential kinetic, metabolomics, and transcriptomics data were collected. Our results suggest that carotenoid production was mainly associated with cell growth and had a positive regulation of central carbon metabolism metabolites associated with glycolysis, the pentose phosphate pathway, the TCA cycle, and amino acids and fatty acids biosynthesis. In the stationary phase, amino acids associated with the TCA cycle increased, but most of the fatty acids and central carbon metabolism metabolites decreased. TCA cycle metabolites such as succinate, fumarate, and α-ketoglutarate were in abundance during both growth and stationary phases. The overall observed metabolic changes in the central carbon metabolism and abundance of TCA cycle metabolites suggest an improvement in the electron transport chain and the provision of the electrons required for the AX synthesis. Transcriptomic data correlated with the metabolic data and found a positive regulation of genes associated with the electron respiratory chain suggesting this to be the main driver for improved AX production in the mutant strain.