Two field experiments were carried out at Arab El-Awammer Research Station, Assiut Governorate during 2016-2017 and 2017-2018 seasons. The present study assessed the effect of intercropping faba bean with some crops on the production, phyllosphere and rhizosphere microorganisms under modern irrigation systems. Two separates experiments were done and each experiment was subjected to one of studied irrigation systems (sprinkler and drip irrigation), Each experiment contained seven treatments of cropping systems (sole faba bean, sole onion, sole garlic, sole fennel; row intercropping of faba bean with onion, garlic and fennel planting both crops on the same row). Results showed that number of branches/plant, seed yield/plant and seed yield/fed. of faba bean was decreased when intercropped with onion, garlic and fennel compared with sole faba bean in both seasons. Drip irrigation produced the maximum yield and its attributes of faba bean as compared with sprinkler irrigation in both seasons. sole onion and garlic gave the highest values of yield/fed. under drip irrigation as compared with intercrop with faba bean and sprinkler irrigation in the both season. However, fennel intercrop with faba bean produced the highest value of yield/fed. under sprinkler irrigation as compared with sole fennel and drip irrigation in the both seasons. The highest LER value of 1.92 was observed with fennel intercrop in faba bean under sprinkler irrigation in first season. Competitive ratio values of onion, garlic and fennel intercrop in faba bean were greater than of sole faba bean in both seasons. Rhizosphere and phyllosphere microorganisms were highly affected by the intercropping and various irrigation systems. Total counts of both bacteria and fungi in plants phyllosphere were high under sprinkle irrigation than drip irrigation system while, drip irrigation was highest in rhizosphere. Sole cropping contained higher microbial number than cropping system. Higher values of the biodiversity index indicate large variation in fungal communities of different plants especially in intercropping.