Moringa oleifera (MO), is greatly appreciated for its high nutritional profile. Germination is an efficient technique to enhance the quality profile of seeds. This study examined the effects of germination and various pre-treatments on MO seeds. MO seeds were subjected to ultrasound dual-frequency 10 and 20 min (US 10 & US 20), microwave 30 and 60 s (MW 30 & MW 60), followed by 15-day germination at 25 °C in a biochemical incubator and subsequent infrared vacuum drying at 70, 60 and 50 °C. Several mathematical modelling were applied, among which Midilli-Kucuk model showed excellent fit R2 ≥ 0.9997, X2 ≤ 0.0030, RMSE ≤ 0.0010, and RSS ≤ 0.000, followed by Newton model respectively. The efficiency of the process varied across different treatment conditions, with values ranging from 3.4 % to 10.27 %, indicating significant differences in energy consumption and water removal rates. Overall in the subsequent drying, US 10 at60 °C significantly improved quality profile of MO seeds (p ≤ 0.05). Antioxidant potency composite (APCI) of germinated MO seeds showed superior APCI in US 10 dried at 60 °C (97.50 %) than control (56.55 %). The principal component analysis (PCA) revealed a significant correlation matrix, explaining 62.14 % of the total variability in the nutritional and bioactive components of MO seed. GC-MS analysis revealed 50 volatile compounds, categorized into 9 chemical classes with acids being the most abundant. SEM analysis showed that 70 °C, drying caused structural degradation, whereas 60 °C preserved seed microstructure more effectively, revealed pre-treatments and temperature-dependent microstructural alterations. These findings demonstrate the efficacy of pre-treatments assisted germination and moderate-temperature infrared vacuum drying as a viable option for improving the nutritional profile of MO seeds. Importantly, this study did not employ formal optimization techniques such as response surface methodology (RSM), energy cost minimization, full techno-economic and life cycle assessments from an engineering perspective. Instead, it sufficiently explored the drying kinetics and the impact of different pre-treatments on the quality profile of MO seeds.