Phoma black stem and leaf spot disease (caused by Phoma medicaginis) not only diminishes forage and seed yield but stimulates production of detrimental phytoestrogens in annual Medicago spp. This study aimed to evaluate relationships between disease development from five isolates of P. medicaginis on 16 cultivars with production of coumestrol and 4′-O-methylcoumestrol. In the presence of P. medicaginis, Sava had the highest coumestrol and 4′-O-methylcoumestrol (640 and 85 mg/kg, respectively) followed by Caliph (253 and 15 mg/kg, respectively). In the absence of P. medicaginis, Jemalong and Paragosa showed highest and lowest coumestrol (137 and 0 mg/kg, respectively). 4′-O-methylcoumestrol was not produced in disease-free plants, but coumestrol was. Disease incidence and severity on leaves and on petiole/stems, and consequent leaf yellowing severity ranged from 5%-98.7%, 0%-100%, 4.4%-98.7%, 1.7%-100%, and 0%-85%. Sava, Paraponto, Harbinger, and Serena were most susceptible, while Tornafield and Caliph were least susceptible. There was significant overall positive correlation of disease incidence/severity factors across cultivars (p < 0.01) with both coumestrol and 4′-O-methylcoumestrol. Jemalong was least responsive and Paragosa and Sava most responsive to coumestrol production following P. medicaginis inoculation. Coumestrol in inoculated Paragosa increased to 373 mg/kg in comparison with 0 mg/kg in controls. These findings are of critical importance towards developing less disease-susceptible annual Medicago spp. producing less detrimental phytoestrogens. Least susceptible cultivars like Tornafield and Caliph can be used to manage yield loss, whilst least responsive cultivars to phytoestrogen production like Caliph also can help to reduce phytoestrogen production.