Minimizing the environmental impact of intensive cropping systems is an urgent task to achieve agricultural sustainability. As microalgae cultivation in nutrient-rich waste streams evolved into a more established and known technology for water reclamation, different applications and valorization proposals for the resulting biomass have emerged, particularly for agriculture. This study aimed to investigate the influence of nutritional stress on carbon, nitrogen, and phosphorous accessibility in different microalgae-bacteria systems for potential use as soil amendment or conditioner. First, oxygenic photogranules and suspended microalgae-bacteria consortia were collected before and after a nitrogen-phosphorous starvation period. After harvesting, biomass was lyophilized and characterized in terms of phosphorous bioavailability and carbon and nitrogen accessibility and complexity following sequential biochemical fractioning coupled with 3D fluorescence spectroscopy. The results showed that bioavailable phosphorous was directly linked to nutrient availability, regardless of the biomass system, in which biomass grown under nutrient-rich conditions presented higher concentrations than starved biomass. On the other hand, photogranules grown under nutrient-rich conditions have a more significant portion of extractible nitrogen (≥ 90% of total nitrogen) than starved photogranules (85-75% of total nitrogen). In contrast, nutrient starvation has the inverse effect on suspended microalgae-bacterial biomass, where the extractible nitrogen part increased from 56% (nutrient-rich) to 63% (nutrient-starved) of total nitrogen. Regarding carbon availability, the portion of extractible carbon increased from 50% (nutrient-rich) to nearly 98% (nutrient-starved) of the total carbon content in all tested samples. Finally, the complexity index of carbon and nitrogen compounds within the most easily extractible fractions was simplified as a response to starvation. This study contributes a first approach to verify the feasibility and differences between suspended and granular microalgae-bacterial biomass systems as a natural solution of non-complex, essential macronutrients for crop growth, which could be utilized after a wastewater treatment process.