SummaryRoot-knot nematodes, Meloidogyne spp., cause great losses to coffee crops in Brazil and worldwide. However, little is known about the physiological changes that these pathogens induce in coffee plants. The present work aimed to compare the physiological variables of coffee seedlings (Coffea arabica ‘Catuaí Vermelho IAC 144’) infected with Meloidogyne paranaensis or M. exigua with healthy coffee plants. Nematode-infected plants showed reductions in height and starch content in roots compared to healthy plants. In addition, the infected plants had a reduction in transpiration, stomatal conductance and CO2 concentration. However, only the coffee seedlings infected with M. paranaensis showed reduction in the rate of photosynthesis. Nematode-infected plants had lower leaf contents of P, K, Mn and Fe when compared to healthy plants. However, only coffee seedlings parasitised by M. paranaensis exhibited lower levels of Ca in the leaves. Therefore, M. paranaensis and M. exigua, with emphasis on M. paranaensis, alter the normal coffee seedling physiology.