Colonization of root cortical cells by arbuscular mycorrhizal fungi leads to marked cytological changes of plastids and mitochondria. Plastids in particular are forming tubular extensions partially connecting individual organelles in a network-like way. These cytological changes correspond to an increased need for plastid and mitochondrial products during establishment and functioning of the symbiosis. The analysis of metabolite and transcript levels in mycorrhizal and nonmycorrhizal roots from Medicago truncatula revealed concomitant changes regarding a number of metabolic pathways. Our results indicate the activation of the mitochondrial tricarboxylic acid cycle and of plastid biosynthetic pathways producing fatty acids, amino acids, and apocarotenoids. These observations provide a general overview of structural and metabolic changes of plastids and mitochondria during colonization of root cortical cells by arbuscular mycorrhizal fungi.