In Australia, root-lesion nematode (RLN; Pratylenchus thornei) significantly reduces chickpea and wheat yields. Yield losses from RLN have been determined through use of nematicide; however, nematicide does not control nematodes in Vertosol subsoils in Australia’s northern grains region. The alternative strategy of assessing yield response, by using crop rotation with resistant and susceptible crops to manipulate nematode populations, is poorly documented for chickpea. Our research tested the effectiveness of crop rotation and nematicide against P. thornei populations for assessing yield loss in chickpea. First-year field plots included canola, linseed, canaryseed, wheat and a fallow treatment, all with and without the nematicide aldicarb. The following year, aldicarb was reapplied and plots were re-cropped with four chickpea cultivars and one intolerant wheat cultivar. Highest P. thornei populations were after wheat, at 0.45–0.6 m soil depth. Aldicarb was effective to just 0.3 m for wheat and 0.45 m for other crops, and increased subsequent crop grain yield by only 6%. Canola, linseed and fallow treatments reduced P. thornei populations, but low mycorrhizal spore levels in the soil after canola and fallow treatments were associated with low chickpea yield. Canaryseed kept P. thornei populations low throughout the soil profile and maintained mycorrhizal spore densities, resulting in grain yield increases of up to 25% for chickpea cultivars and 55% for wheat when pre-cropped with canaryseed compared with wheat. Tolerance indices for chickpeas based on yield differences after paired wheat and canaryseed plots ranged from 80% for cv. Tyson to 95% for cv. Lasseter and this strategy is recommended for future use in assessing tolerance.