In pea (Pisum sativum L.) production, Didymella pinodes (Berk. & A. Bloxam) Petr. is the most damaging aerial pathogen globally. In two completely randomized pot experiments with four replicates, we studied the effects of D. pinodes infection interaction with three symbiotic treatments (Rhizobium leguminosarum biovar viciae, arbuscular mycorrhizal fungi (AMF) and co-inoculation of both) and a non-symbiotic control on one or two pea cultivars. Grain yield and yield components of pea, uptakes and physiological efficiencies of N and P and nitrogen fixation were recorded. The results show that there were significant interaction effects among treatments. Therefore, productivity of crops and their uptakes and efficiencies of N and P are dependent on plant health conditions, effectiveness of microbial symbionts and response of pea genotypes. For cv. Protecta inoculated with both symbionts, pathogen infection compared to healthy plants significantly enhanced P acquisition. Overall, plants inoculated with rhizobia alone had higher grain yield by 20–30% and nitrogen fixation by 20–25% than in dual symbiosis independent of plant health conditions. In conclusion, aerial pathogen, pea genotypes and microbial symbionts interactions modified N and P uptake and their efficiencies, which can lead to improving final grain yield quantity and quality in a sustainable farming system.