In this study, the high-lipid biomass accumulation of the microalga Micractinium sp. IC-76 in a 110-L flat panel photobioreactor was studied in detail. The productivity of microalgae biomass during phototrophic cultivation was 35.6 ± 1.5 mg L−1 d−1. The maximum content of neutral lipids with a high saturated and monounsaturated fatty acid content (44.1%) was observed on the 17th day of cultivation, which was optimal for processing into biodiesel. The main fatty acids of lipids were C16:0, C16:2, and C18:2, with contents of 26.0, 15.6 and 29.8%, respectively. The enzymatic transesterification of Micractinium sp. IC-76 lipids using cross-linked enzyme aggregates (CLEAs) of Burkholderia cepacia lipase as biocatalysts was optimized by response surface methodology (RSM) to produce fatty acid methyl esters (FAMEs). This model determined that the optimum conditions for enzymatic transesterification of microalgal lipids with a maximal FAME yield of 92.3 ± 1.5% were a temperature of 38 °C, a methanol to oil molar ratio of 1:3.1, a CLEA of 9.1% and a water content of 2.5% relative to the oil weight. This model has a high correlation with the experimental data and can be used to model the production of FAMEs from the lipids of Micractinium sp. IC-76 during process scaling.