This article proposes an easy, quick, and efficient microwave method for the routine laboratory extraction of lipids from wet microalgae paste. A microwave synthesis instrument is used, and time and temperature are optimized using a central composite design. A chloroform/methanol mixture (2:1 v/v) is used as extractor solvent and the ideal condition is 1 min of microwave irradiation at 80 °C using power mode at 300 W. The scanning electron microscopy (SEM) analysis shows extensive cell damage leading to cracking, fragmentation, and large debris in a shorter treatment time. In addition, the fatty acids profile shows that microwave irradiation method has no degrading effect on the extracted fatty acids. The extraction by microwave achieves a significantly higher yield (33.6 ± 2.6%) with only 1 min of extraction time than conventional ultrasonic extraction (20 min, 25 °C, 28.51 ± 0.8% yield) from wet Nannochloropsis oculata biomass. Next, the efficiency of the extraction method in is evaluated in terms of species variation by applying it to the algal paste of Amphora coffeaeformis, Chaetoceros gracilis, and Isochrysis galbana. The lipid content obtained from A. coffeaeformis, C. gracilis, and I. galbana is 16.27 ± 1.5, 22.31 ± 2.5, and 19.87 ± 2.4%, respectively. Thus, the microwave method is successfully applied to algal paste. Practical Applications: The microalgal cell wall disruption is an important and complex stage and effective methods of disruption are fundamental to extracting lipids. This study shows an easy, quick, and efficient microwave method for application in routine laboratory extraction of lipids from wet microalgae pastes. A microwave compact instrument is used and the ideal condition is 1 min of microwave irradiation. The method proves to be robust against variation in mass achieved and significantly higher yield in a shorter time than ultrasonic extraction (conventional method). The microalgal cell disruption is an important and complex stage. The use of microwaves to induce cell disruption in wet biomass proves to be efficient for lipid extraction with only 1 min of extraction time. The method is applied successfully to wet microalgae pastes with different cell walls and the microwave radiation does not degrade the extracted fatty acids.