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Due to the potential to enhance soil productivity and plant growth, biological fertilizers have recently been considered an alternative source for soil, water, and crop-contaminating chemical fertilizers in sustainable agriculture. The importance of different fertilizer sources on quantitative and qualitative traits of <i>Syrian cephalaria</i> (<i>Cephalaria syriaca</i> L.) was explored in an experiment based on a randomized complete block design during the 2015–2016 growing season. The maximum grain yield (9.97 g/plant) and biological yield (24.57 g/plant) were obtained from the application of <i>Azotobacter</i> + chemical fertilizer treatment, but the maximum oil percentage (25.23%) and oil yield (2.41 g/plant) were observed in the plants treated with <i>Azotobacter</i> + vermicompost. The plants treated with <i>Azotobacter</i> + chemical fertilizer exhibited the highest 1000 seed weight (15.03 g). Application of <i>Azotobacter</i> + vermicompost increased chlorophylls <i>a</i>, <i>b</i>, and total by 2.06, 1.96, and 4.02% versus <i>Azotobacter</i> treatment alone, respectively. The treatment of <i>Azotobacter</i> + manure increased total phenol, flavonoids, and DPPH antioxidant activity by 27.89, 0.56, and 53.16% versus the treatment of <i>Azotobacter</i> + chemical fertilizer. The integrated application of different fertilizer sources had an optimal effect on the uptake of trace elements (Cu, Fe, and Zn) so that the treatment of <i>Azotobacter</i> + vermicompost increased their concentrations. Due to the positive effect of integrated application of different fertilizer sources on improving the studied traits of <i>Cephalaria</i>, it is recommended to replace chemical fertilizers with combined fertilizers including organic and biological inputs to enhance the efficiency of crops, reduce environmental pollution, and move towards sustainable agriculture.