Lygus bugs and Botrytis fungal pathogen, the causal agent of chocolate spot in faba bean, can cause necrotic spots on faba bean seeds, thereby reducing market value. The mid-pod stage is the most susceptible stage for chocolate spot development and Lygus infestation in faba beans. Therefore, we hypothesised that the concomitant presence of Lygus spp. and Botrytis spp. might increase seed necrosis. Hence, the study was conducted to determine (i) the spatial and local distribution of chocolate spot and Lygus spp. in central and southern Alberta, and (ii) the association of chocolate spot disease severity and Lygus abundance. Chocolate spot and Lygus were present in all the counties surveyed. Chocolate spot had a negative association with Lygus abundance, but only the latter was significantly associated with seed necrosis. Botrytis spp. were frequently isolated from seeds despite the lack of expression of chocolate spot on the foliage. No significant effect of Lygus abundance on Botrytis isolation from seeds was found. Therefore, seed quality losses can occur both due to the fungal pathogen and the insect, which likely occupy different niches influenced by microclimate. Economic thresholds and management strategies will be required to keep insect populations and disease progression under check.