The aim of this work was to analyse and compare indigenous arbuscular mycorrhizal colonisation (AMC) in relation to growth and total soluble carbohydrates (TSC) in two major, physiologically contrasting crop species: maize (Zea mays L.) and sunflower (Helianthus annuus L.). In order to promote contrasting TSC concentrations, we modified the radiation source by shading and the carbohydrate sink by manipulating reproductive sinks at different phenological stages during the grain-filling period in two field experiments. We assessed plant dry matter, TSC in stems, and root AMC from flowering until final harvest. AMC during the grain-filling period decreased in maize and increased in sunflower. A sink limitation increased AMC in maize, and reduced it in sunflower. A source limitation decreased AMC in both species, especially in sunflower. AMC was positively related to TSC in maize, but negatively in sunflower. The relationship was affected by shading in sunflower, but not in maize. In both species, a different linear model described the relationship between AMC and TSC in plants submitted to the removal of the reproductive organs. The results highlight the role of carbohydrates in mediating mycorrhizal formation, and show for the first time the opposite AMC–TSC relationships in maize and sunflower.