Papaver somniferum L. produces therapeutically-useful alkaloids like morphine, codeine, papaverine, and thebaine that accumulate in the latex of its capsule. Apart from its alkaloids, the edible seeds of the plant have high nutritional value and culinary use, with the seed oil being rich in the health-promoting unsaturated fatty acids. Sujata is low alkaloid-producing latex-less culinary variety of P. somniferum developed from an alkaloid-rich gum harvest parent (Sampada) for curtailing the narcotic menace of morphine and opium (dried latex). Earlier, it has been shown that the expression of stearoyl-acyl-carrier protein desaturase (PsSAD) in the young capsule and the proportion of unsaturated fatty acids in the seeds are higher in Sujata as compared to Sampada. Here, we studied bacterial endophytes isolated from Sujata tissues for their role in defining the fatty acid (saturated stearic versus unsaturated oleic) profile in its leaves and seeds. Besides, a potyvirus infecting P. somniferum was characterized through its coat protein gene sequencing and transmission electron microscopy and the two genotypes (Sujata and Sampada) contrasting in their phenotypes (oil/fatty acid, alkaloid and latex profiles) were compared for their susceptibility towards it through indicator plant- and qRT-PCR-based virus infectivity assays. In both the assays, Sujata was found to have higher susceptibility to the potyvirus, as compared to Sampada. The most plausible reason for this could be the higher PsSAD expression in the leaves of Sujata, which resulted in higher relative levels of oleic acid and lower relative levels of stearic acid in its leaves as compared to that of Sampada.