Intercropping and biofertilizer are thought to be strategies for reducing the risks of agricultural production and enhancing yield and quality in developing sustainable agriculture. Hence, two field experiments were carried out with factorial arrangement based on a randomized complete block design with three replications, to evaluate the effects of fertility and cropping systems on quality of safflower in 2015 and 2016. Treatments included nutrient levels (100% chemical fertilizers, 60% and 30% chemical + biological fertilizers and no fertilizer) and safflower and faba bean sole cropping, intercropping systems of them with ratios of 1:1 and 2:1. Results revealed that the integrated use of chemical and biofertilizers in intercropped plants caused to increasing yield components of safflower for both years. The highest unsaturated fatty acids, protein and oil content were achieved in 60% chemical plus biofertilizers. Also, between intercropping systems, ratio of 1:1 and the combinative application of chemical and biofertilizers had the highest land equivalent ratio. Values of actual yield loss showed an advantage of 20 to 98 % from intercropping due to recovery made by intercrops. Therefore, it was concluded that intercropping (safflower / faba bean) with integrated use of the reduced chemical and biological fertilizers, improved growth and quality of safflower.