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BACKGROUND Nitrogen (N) limitation is the most common strategy used to accumulate energy‐rich compounds in microalgae. However, this condition reduces the microalga growth rate and biomass, lipid and carbohydrate productivities. In this work, a semi‐continuous operation strategy combined with N feast–famine cycles were investigated in order to increase the lipid, carbohydrate and biomass contents in the microalga Scenedesmus obtusiusculus AT‐UAM. RESULTS Growth and lipid productivity were evaluated in a flat‐panel photobioreactor (FP‐PBR) under controlled conditions, through 72 and 24 h N feast–famine cycles at different N concentrations (6, 12 and 24 mg N L−1). The highest accumulation of microalgal biomass, lipid and carbohydrate (550 ± 28, 139 ± 4 and 198 ± 7 mg L−1 d−1) was obtained for 24 h cycles at 12 mg N L−1 and were up to ~2.4 times compared to that of 72 h N feast–famine cycles. This strategy was also applied in a bubble column photobioreactor (BC‐PBR) located in a greenhouse. Here, biomass productivities obtained under a semi‐continuous operation for 24 h N feast–famine cycles with 6 and 12 mg N L−1 were 536 ± 27 and 667 ± 33 mg L−1 d−1, respectively. The maximum productivity of lipid and carbohydrate reached 142 ± 10 and 169 ± 14 mg L−1 d−1 with 12 mg N L−1, respectively. CONCLUSION The studied N feast–famine cycles and semi‐continuous operations increased the productivity of biomass and lipids in S. obtusiusculus AT‐UAM. © 2021 Society of Chemical Industry (SCI).