Under an adequate supply of nitrogen (N) and phosphorus (P), the cyanobacterium Synechocystis sp. PCC 6803 produced a high biomass yield but with a low storage level of glycogen and poly(3-hydroxybutyrate) (PHB). In contrast, deprivation of N or P stimulated accumulation of glycogen and PHB, but reduced biomass yield. In addition, deprivation of N or P had no apparent effect on total lipid accumulation. Here, we examined how partial supply of N or P has effects on the biomass yield and production of glycogen, PHB, and lipids. The N or P supply in the culture media was orderly decreased from 100% (set according to the standard BG11 medium) to 50, 35, 20, 10, and 0%. A 100% supply of both N and P produced biomass of up to 1.4 g L−1, while a 35–50% N supply slightly reduced the biomass to 1.2–1.3 g L−1, and no apparent change in the biomass was detected under a 20–50% P supply. A maximum glycogen accumulation of 51.8% (w/w dry weight; DW) was obtained under 20% P supply, while the maximum PHB storage of 6.3% (w/w DW) was obtained with 10% P supply. Lipid accumulation peaked at 12.7% (w/w DW) under 0% P supply. The maximal co-production of these three bioproducts was obtained under 20% P supply at 765 mg L−1 which is the sum of 72 mg L−1 PHB (corresponding to 5.1% w/w DW PHB), 618 mg L−1 glycogen (43.8% w/w DW glycogen), and 75 mg L−1 lipid (5.3% w/w DW lipid) from the total biomass production of 1.4 g L−1. The glycogen production (618 mg L−1) was higher than those previously reported for Synechocystis. The results indicated that a proper adjustment of initial N and P supplies in the culture is crucial for maximal production of these three bioproducts by Synechocystis.