This study aimed to investigate the nutritional character (carbohydrates, proteins, pigments, and phycocyanin), total antioxidant capacity (TAC) and the capability of simulating the growth of Lactobacillus rhamnosus of different extracts from C. vulgaris and A. platensis by means of the application of conventional aqueous extraction procedure and pulsed electric field (PEF) extraction technology. It was confirmed a significantly improved nutritional profile of Chlorella and Spirulina extracts obtained by PEF technology pre-treatment (3 kV/cm, 100 kJ/kg), with specifically higher values in total carbohydrate, Chlorophyll a, Chlorophyll b, and carotenoids content, and TAC. Additionally, Spirulina PEF extract showed a probiotic's growth-stimulating capability of 1 log10 cycle when fermented by Lactobacillus rhamnosus, with a metabolomic profile specifically rich in bioactive short chain fatty acids (SCFAs) and organic acids (3-phenyl lactic acid). The present study points out the applicability of PEF extraction technology under optimized conditions to improve the nutritional and functional character of microalgae and cyanobacterial-derived ingredients.