Photobioreactor geometry, light distribution and nutritional regime determine not only how much biomass is produced, but also the physiological trajectory followed by microalgal cultures under changing nutrient availability. Here, Nannochloropsis gaditana was cultivated in a custom 3D-printed flat-panel photobioreactor platform in which the illuminated surface was kept constant while optical path length, culture volume and illuminated surface-to-volume ratio (ISVR) were varied. Six ISVR values, ranging from 6 to 65 m² m⁻³, were combined with three nitrate doses, 0, 28 and 140 mg NO₃⁻ per cultivation unit, generating 18 final biomass samples from a common nutrient-replete inoculum. This design enabled the simultaneous evaluation of productivity, cytometric behaviour, elemental composition, pigment remodelling, amino acid abundance, crude lipid accumulation and fatty acid profiles. Nitrate availability was the dominant driver of biomass composition, whereas ISVR acted as a geometry-dependent modulator, especially when nitrogen was available. Productivity per cultivation unit reached its maximum at intermediate ISVR values, while volumetric productivity increased with ISVR, showing that reactor performance can be interpreted differently depending on the normalization criterion. Under nitrate deprivation, N. gaditana maintained substantial biomass production, but this was accompanied by strong nitrogen dilution, chlorophyll a loss, reduced amino acid accumulation, higher carbon and crude lipid fractions and enrichment in C16:0 and C16:1 fatty acids. By contrast, nitrate-sufficient cultures, particularly under lower effective light pressure, retained part of the inoculum green colour, and the initial profile rich in amino acids and eicosapentaenoic acid (EPA). EPA behaved differently from stress-associated storage fatty acids, supporting its association with active growth and membrane-rich biomass rather than with general lipid accumulation. Overall, these results show that nitrate management and photobioreactor light distribution can redirect N. gaditana towards contrasting compositional profiles, from protein- and EPA-oriented biomass to carbon- and storage-lipid-enriched biomass, depending on the intended application.