The aim of this study was to analyze the metabolism of storage materials in germinating tomato (Solanum lycopersicum) seeds and to determine whether it is regulated by light via phytochromes. Wild type, single and multiple phytochrome A, B1 and B2 mutants were investigated. Imbibed seeds were briefly irradiated with far-red or far-red followed by red light, and germinated in darkness. Triacylglycerols and starch were quantified using biochemical assays in germinating seeds and seedlings during the first 5 days of growth. To investigate the process of fat-carbohydrate transformation, the activity of the glyoxylate cycle was assessed. Our results confirm the role of phytochrome in the control of tomato seed germination. Phytochromes A and B2 were shown to play specific roles, acting antagonistically in far-red light. While the breakdown of triacylglycerols proceeded independently of light, phytochrome control was visible in the next stages of the lipid-carbohydrate transformation. The key enzymes of the glyoxylate cycle, isocitrate lyase and malate synthase, were regulated by phytochrome(s). This was reflected in a greater increase of starch content during seedling growth in response to additional red light treatment. This study is the first attempt to build a comprehensive image of storage material metabolism regulation by light in germinating dicotyledonous seeds.