This work focuses on a culture strategy that combines high biomass production and lipid accumulation in the green microalgae Raphidocelis subcapitata immobilized in alginate gel in order to obtain high lipid productivity for biodiesel production. The study of the effects of nitrogen and phosphorus deficiency on lipid accumulation and biomass production in immobilized microalgae showed that both conditions (N− and P−) promoted lipid accumulation in the microalgae. The lipid contents achieved under nitrogen (31.7% ± 3.2% (dcw)) and phosphorus (19.4% ± 1.9% (dcw)) deficiency conditions were higher than those obtained in the complete medium (control) (14.9% ± 1.5% (dcw)). The highest lipid productivity was recorded under nitrogen deficiency conditions (PL = 11.1 ± 1.1 mg/L/day). This indicated that nitrogen deficiency was more effective than phosphorus deficiency in terms of triggering lipid accumulation in the microalgae. However, the conditions for inducing lipid accumulation (N− or P−) resulted in slower growth. In order to address this issue and achieve high lipid productivity, a two-step culture strategy was used. Immobilized R. subcapitata was cultivated under optimal concentrations of nitrogen and phosphorus to achieve a high biomass concentration. Thereafter, the beads containing the microalgae were transferred to a culture medium under nitrogen deficiency conditions in order to induce lipid accumulation. The concentrations 1.5 g/L of NaNO3 and 20 mg/L of K2HPO4 were determined as being the optimal concentrations for growth, and they produced the highest biomass production rates (µm max = 0.233 ± 0.023 day−1 and µm max = 0.225 ± 0.022 day−1 for NaNO3 and K2HPO4, respectively) from all of the concentrations studied. With the two-step culture strategy, immobilized R. subcapitata accumulated 37.9 ± 3.8% of their dry weight in lipid and reached a lipid productivity value of PL = 40.3 ± 4.0 mg/L/day under nitrogen deficiency conditions. This value was approximately 3.6 times higher than that obtained in the direct culture of cells under nitrogen deficiency conditions (PL = 11.1 ± 1.1 mg/L/day).