Karrer revealed the long chain of conjugated double bonds in plant pigments known as carotenoids and how they are converted to vitamin A in the body. He also isolated the yellow pigment flavin, studied its light stability, and showed how it becomes the coenzymes FMN and FAD. His work clarified the biochemical roles of vitamins A and B2, which are essential for vision, growth and energy metabolism. This knowledge enabled the diagnosis of deficiency diseases and the development of fortified foods, providing a scientific way to combat malnutrition in an era when food shortages were common.

By combining solvent extraction with chromatography, Karrer obtained pure crystals of many carotenoids including β-carotene. UV-visible spectroscopy showed that a chain of eleven or more conjugated double bonds accounts for strong light absorption and antioxidant properties. Through chemical reduction he cleaved the carotene skeleton and proposed the biosynthetic pathway leading to vitamin A (retinol). For riboflavin he solved the structure consisting of an isoalloxazine ring and a ribitol side chain, demonstrating that ATP-dependent phosphorylation forms FMN and subsequent adenylation yields FAD. These achievements influence clinical diagnosis of vitamin deficiencies, food analytical methods and pigment chemistry in photosynthesis.

Karrer refined the Kuhn reaction, identifying the terminal aldehyde positions of C40 carotenoids via ozonolysis followed by oxime derivatization and analysis by NMR and optical rotation. He traced the in vivo 15,15′-dioxygenase cleavage of β-carotene, proposing that the split products convert to retinal and feed into rhodopsin biosynthesis. For riboflavin he employed chemical methylation and pKa determination to fix the basic center at N-10, and measured electron-transfer rates in the photoexcited state using visible-pump/IR-probe spectroscopy. These quantitative data supported kinetic modeling of flavins as redox coenzymes.