Microalgae offer a sustainable platform for biotechnology due to their rapid growth and ability to accumulate high-value metabolites such as lipids, proteins, and carbohydrates. This study investigates the biochemical and morphological responses of Chlorella vulgaris and Scenedesmus incrassatulus across different growth phases and under nitrogen (N) and phosphorus (P) deficiency. Molecular identification and phylogenetic analysis confirmed the taxonomic status of both species. Scanning Electron Microscopy (SEM) combined with Energy Dispersive X-ray Spectroscopy (EDS) revealed species-specific surface structures and elemental composition. S. incrassatulus exhibited a compact, granular morphology, while C. vulgaris showed a smoother, colonial structure. EDS analysis demonstrated higher potassium and phosphorus levels in C. vulgaris, whereas S. incrassatulus presented elevated calcium and magnesium contents. Biochemical profiling indicated a metabolic shift during the stationary phase, with reduced protein synthesis and increased lipid and carbohydrate accumulation. Under nitrogen deficiency, C. vulgaris achieved the highest lipid content (53.68%), while S. incrassatulus reached 45.86%. Carbohydrate accumulation was also prominent during the stationary phase, with values of 49.18% for C. vulgaris and 47.99% for S. incrassatulus. Protein content was highest in the exponential phase and declined under nutrient stress. Elemental analysis via Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES) confirmed species-specific macronutrient and trace element profiles, supporting EDS data. These findings highlight the adaptive biochemical and structural traits of the two microalgae species, reinforcing their potential in biofuel production, sustainable agriculture, bioremediation, and environmental applications. Future work should focus on optimizing cultivation conditions and exploring genetic approaches to maximize metabolite yields for industrial-scale applications.