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Multi-product biorefineries, which transform biomass feedstocks into multiple valuable bio-based products, are pivotal for transitioning from a fossil-based economy to a sustainable circular bioeconomy. This work proposes a processing pipeline for fractionating the macrocomponents of Nannochloropsis oceanica, which can serve as a basis for multi-product microalgae biorefineries. It consists of high-pressure homogenization (1200 bar, 1 cycle) to permeabilize the cells, and sequential membrane processing (0.2 µm dia-microfiltration followed by 100 kDa ultrafiltration) and ethanolic extraction (60 mL ethanol/g dry weight, 1 h) to fractionate the disrupted biomass. This biorefinery resulted in four final fractions: (1) enriched in water-soluble proteins (39.0 ± 2.8% w/w proteins; 10.7 ± 0.8% w/w carbohydrates); (2) remaining soluble components (5.7 ± 0.4% w/w proteins; 4.3 ± 0.9% w/w carbohydrates); (3) lipid-rich extract (62.4 ± 5.8% w/w lipids); and (4) non-extracted components (11.8 ± 4.5% w/w lipids), with mass recovery yields of 23.2 ± 2.1%, 6.9 ± 1.0%, 10.6 ± 1.9%, and 60.4 ± 4.1%, respectively. The ultrafiltration protein selectivity was not optimal, despite yielding a 2.6 times more concentrated fraction. Lipid extraction yield (35–60%) and purity (56–68%) were highly affected by the water content of the microfiltration retentate. Overall, 10.0 ± 0.9% of the proteins, 9.7 ± 1.8% of the carbohydrates, and 42.4 ± 13.4% of the lipids of N. oceanica were recovered in fractions 1, 2, and 3, respectively.