Four strains of Bacillus amyloliquefaciens with high proteolytic, fibrinolytic, and angiotensin converting enzyme (ACE) inhibitory activities were used to make Bacillus-koji suitable for the production of functional doenjang. Volatile compounds in Bacillus-koji doenjang were analyzed by headspace-solid phase microextraction-GC-MS (HS-SPME-GC-MS) to compare the aroma profile with those of commercially produced doenjang made with traditional meju and with modified koji. Extraction temperatures for SPME were adjusted to 30 and $90^{circ}C$. Commercial samples contained significantly more esters than Bacillus-koji doenjang and demonstrated a more complex volatile compound profile. Pentanoic acid, butanoic acid, or 2/3-methyl butanoic acid, known as off-flavor compounds in doenjang, were not detected in one of the Bacillus-koji doenjang when extracted at $30^{circ}C$. From the sensory test results, the cheese character was less intense in Bacillus-koji doenjang than commercial samples, although not all sensory properties projected a significant difference.