We aimed to develop a consortium of starter culture of effective microorganisms to prepare doenjang, a traditional Korean fermented food. Different ratios of Bacillus subtilis TKSP 24 (B), Aspergillus oryzae complex (A), Rhizopus nigricans (also named as Rhizopus stolonifera) (R), and Mucor racemosus 15 (M15) were selected as meju starter cultures to produce doenjang with improved quality. Microbial strain combinations (B: A: R and B: M15: R) were mixed separately at three different ratios [1:1:1 (w/w), 1:0.5:1.5 (w/w), and 1:1.5:0.5 (w/w)] to prepare BAR-1, BAR-2, BAR-3, BM15R-1, BM15R-2, and BM15R-3 doenjang samples. Quantitative analyses included free amino acids, free sugar, volatile and non-volatile organic acids, cellular antioxidant activity along with the presence of biogenic amines and aflatoxins, and microbial counts. Total free amino acids responsible for the sweet taste of doenjang were highest in BAR-2 (322.50 mg/100 g) and BM15R-3 (320.07 mg/100 g). Total volatile organic acid was highest in BAR-1 compared to other preparations. All doenjang samples had biogenic amines, especially histamine, below the toxicity level (500 mg/kg). Also, the aflatoxin and hazardous microbial count in the tested doenjang samples were below the level of toxicity. The findings suggest that use of multiple microbial strains in combination with R. nigricans as a starter culture could be a novel and effective approach to improve the nutrition and safety of fermented soybean food products of doenjang.