Nematode migration, feeding site formation, withdrawal of plant assimilates and activation of plant defence responses have a significant impact on plant growth and development. Plants display intraspecific variation in tolerance limits for root-feeding nematodes. Although disease tolerance has been recognised as a distinct trait in biotic interactions of mainly crops, we lack mechanistic insights. Progress is hampered by difficulties in quantification and laborious screening methods. We turned to the model plant Arabidopsis thaliana, since it offers extensive resources to study the molecular and cellular mechanisms underlying nematode-plant interactions. We established through imaging of tolerance-related parameters that green canopy area was an accessible and robust measure for assessing damage as the consequence of cyst nematode infection. Subsequently, we developed a high-throughput phenotyping platform to non-destructively measure the green canopy area growth of 960 A. thaliana plants simultaneously. We show that A. thaliana can be used to study tolerance limits of plants to cyst and root-knot nematodes. Although our results can be adequately modelled with classical tolerance limit quantifying methods, real-time monitoring allowed more accurate growth rate measurements. Based on our findings, we believe that our phenotyping platform will enable further studies into the underlying mechanisms of tolerance to below-ground biotic stress.