Blue-green light is known to maximize the degree of fatty acid (FA) unsaturation in microalgae. However, knowledge on the particular waveband responsible for this stimulation of FA desaturation and its impact on the pigment composition in microalgae remains limited. In this study, Acutodesmus obliquus was cultivated for 96 h at 15°C with different light spectra (380–700 nm, 470–700 nm, 520–700 nm, 600–700 nm, and dark controls). Growth was monitored daily, and qualitative characterization of the microalgal FA composition was achieved via gas chromatography coupled with electron impact ionization mass spectrometry (GC-EI/MS). Additionally, a quantitative analysis of microalgal pigments was performed using high-performance liquid chromatography with diode array detection (HPLC-DAD). Spectra that included wavelengths between 470 and 520 nm led to a significantly higher percentage of the polyunsaturated fatty acids (PUFA) 18:3 and 16:4, compared to all other light conditions. However, no significant differences between the red light cultivations and the heterotrophic dark controls were observed for the FA 18:3 and 16:4. These results indicate, that exclusively the blue-green light waveband between 470 and 520 nm is responsible for a maximized FA unsaturation in A. obliquus. Furthermore, the growth and production of pigments were impaired if blue-green light (380–520 nm) was absent in the light spectrum. This knowledge can contribute to achieving a suitable microalgal pigment and FA composition for industrial purposes and must be considered in spectrally selective microalgae cultivation systems.