This research was conducted to evaluate quality changes in traditional Doenjang and manufactured Doenjang during a storage period of 8 weeks. Low-salt Doenjang and commercial Doenjang were purchased from different manufacturers and proximate analysis as well as changes in isoflavone, polyphenol, flavonoid contents of the samples were investigated using a mass spectrophotometer. The salinity of traditional Doenjang, low salt Doenjang, and commercial Doenjang were 13.2±1.15, 7.17±2.74, 10.67±0.35%, respectively and the salt concentrations of the soybean pastes did not change during storage. After 8 weeks at 35℃, chromatic values of all the paste samples decreased somewhat, with traditional Doenjang exhibiting fewer changes as compared to manufactured Doenjang. Amino acid nitrogen, acidity, microbial population all tended to increase with time, although some samples showed fluctuations during the test period. Moreover, the total isoflavone contents of traditional Doenjang increased with storage time while that of manufactured Doenjang tended to decrease. The isoflavone aglycone was shown to be the highest in traditional Doenjang, while isoflavone glycoside was abundant in manufactured Doenjang. Total flavonoid contents showed similar trends regardless of samples; initial contents of total flavonoid was 0.6 mg/g which increased to more than twice to 1.4 mg/g at the end of storage period. Composition profile of Doenjang extracts was analyzed using UPLC-Q-ToF