The quality of microalgae-bacteria biomass as an organic soil fertilizer may depend on the biomass’s microbial composition, morphology, and growth history. This study aims to characterize the molecular complexity and bioaccessibility of organic matter, nitrogen, and phosphorus from microalgae-bacteria aggregates with different morphologies (flocs and granules) grown under nutrient-abundant and starvation conditions. A biochemical fractionation method was used based on sequential chemical extraction and fluorescence spectroscopy. Microalgae-bacteria aggregates were cultured and collected from photobioreactors using contrasting growth conditions to generate (i) loose flocs, (ii) consolidated flocs, (iii) smooth granules, and (iv) filamentous granules. The organic matter, nitrogen, and phosphorus from consolidated flocs were mostly extractable, accounting for up to 94% of their total content. In contrast, the organic matter from loose flocs was up to 50% non-extractable. The extractability of loose flocs was improved under starvation conditions. All microalgae-bacteria aggregates showed a low structural complexity, corresponding to an abundance of simple microbial-related constituents like tyrosine and tryptophane. Differences between the gradients of bioaccessibility for each microalgae-bacteria structure were related to the abundance of microorganisms and their metabolic products. The findings of this study have implications for the development of sustainable and environment-friendly organic fertilizers. Graphical Abstract