This study aimed to explore the impact of ultrasound (US) and microwave (MW) treatments at varying power levels (200W-500W for ultrasound; 400W-800W for microwave) and durations (10–30 minutes for ultrasound and 20-40 seconds for microwave) on the extraction, physicochemical, techno-functional, and intermolecular characteristics of bathua starch. It was found that both ultrasound-assisted and microwave-assisted extraction significantly altered the functional, thermal, physicochemical, and morphological properties of the starch. The extraction yield increased with higher power levels during ultrasonication, with the highest yield being 49.91% (w/w) at 350W for 30 minutes. The control method without pretreatment had the lowest yield of 42.55%, showing a significant difference (p < 0.05). For microwave extraction, the highest yield was 49.12% at 800W for 30 seconds. Pretreatments of US (350W for 30 minutes) and MW (600W for 30 seconds) resulted in higher L* values for the extracted starch (97.06 and 96.62, respectively) compared to the control (96.15), which was statistically significant (p < 0.05). Ultrasound-assisted extraction (UAE) generally exhibited higher solubility (SP) than the control, except for the sample treated at 200W for 10 minutes. The highest water absorption capacity (WAC) and oil absorption capacity (OAC) for ultrasound-extracted starch were 1.97 g/g and 2.39 g/g (at 350W for 30 minutes), with both statistically significant (p < 0.05) compared to the control. Additionally, UAE starches showed decreased relative crystallinity. Based on these findings, the sample treated at 350W for 30 minutes is recommended for extraction due to its superior functional properties, beneficial for applications like emulsion and food product formulation.