We compared the plasma membrane, tonoplast and mitochondrial Mg-ATPase activities of microsomes isolated from mycorrhizal and non-mycorrhizal sunflower (Helianthus annuus L.) and onion (Allium cepa L.) roots during a time-course experiment (21–60 d). No significant difference was observed between the protein levels of root microsomes from mycorrhizal and non-mycorrhizal sunflower. However, the protein content of microsomes obtained from mycorrhizal onion roots increased when the symbiosis was well established (more than 50 % of root length colonized by the arbuscular mycorrhizal fungus). Kinetic studies revealed that vanadate-sensitive (plasma membrane-associated) ATPase activity of sunflower root microsomes increased with mycorrhizal colonization. However, the vanadate-sensitive ATPase activity of microsomes from mycorrhizal onion roots decreased compared with those from non-mycorrhizal controls. Increased activity of nitrate (tonoplast-associated) and azide (mitochondrial membrane-related)-sensitive ATPase activities was detected in extracts obtained from 45– and 60–d-old mycorrhizal onion plants. A slight increase in azide-sensitive ATPase activity was detected in microsomes of mycorrhizal sunflower. The existence of different physiological and biochemical strategies in sunflower and onion in relation to the establishment of this mutualistic symbiosis is discussed.