In this study, changes in the bioactive properties, phenolic profiles, fatty acids, lipid indices of the water bath and sonication processes applied to roasted and unroasted bitter orange seeds were revealed by spectrophotometric and chromatographic techniques. The total phenolic amounts of roasted bitter orange seeds treated in a water bath (WB) were defined to be between 56.11 (25 min) and 65.43 mgGAE/100 g (control), while the total phenolic quantities of sonicated bitter orange seeds are characterized between 59.03 (control) and 66.01 mg/100 g (50 min). The total flavonoid contents of unroasted bitter orange seeds treated in WB and ultrasonic bath (UB) were depicted between 70.60 (25 min) and 77.50 mg/100 g (50 min) to 72.98 (50 min) and 83.69 mgGAE/100 g (25 min), respectively. While total flavonoid quantities of roasted bitter orange seeds treated in WB are defined between 73.21 (control) and 97.26 mg/100 g (50 min), total flavonoid amounts of roasted bitter orange seeds treated in a ultrasonic bath were assessed to be between 58.45 (control) and 102.02 mg/100 g (50 min). Catechin amounts of unroasted bitter orange seeds extracted by the WB and UB extraction systems were established between 15.88 (25 min) and 37.41 (control) to 12.81 (control) and 39.33 mg/100 g (50 min), respectively. Nutritive Value Index (NVI) results of citrus seed oils processed in WB and UB were defined to be between 0.96 (50 min) and 1.20 (control) to 1.14 (control) and 1.22 (50 min), respectively. In general, the total phenolic and total flavonoid contents of unroasted bitter orange seeds increased in WB and UB treatments compared to the control depending on the sonication time. The oleic and linoleic acid contents of oils extracted from seeds treated in WB and UB were close to each other depending on the finishing times.