The increasing use of chemical fertilizers has raised issues of land deterioration and agricultural system sustainability. The use of microalgae biomass could be beneficial in the soil due to its organic matter, minerals, and bioactive compounds. This paper deals with comparing three different microalgae species, namely Chlorella vulgaris, Arthrospira platensis, and Nannochloropsis oculata, concerning their potential for agricultural applications based on their physicochemical, morphological, thermal, and structural characteristics. Microalgae biomass mostly consists of organic matter. The content rate varied from 80.4 ± 2.6% to 96.8 ± 2.65%, while the organic carbon content ranged from 46.63 ± 1.50 to 56.14 ± 1.53%. Microalgae composition varied, with N. oculata having the largest concentration of K, Na, Ca, P, Fe, Mn, and Zn, while A. platensis had the highest amounts of Mg and nitrate. Cation exchange capacity varied in the samples from 7.88 ± 0.24 to 12.64 ± 0.55 meq/100 g, and the water holding capacity was highest for A. platensis (2.5 ± 0.13 g H₂O/g dry weight). The pH of both A. platensis and N. oculata was neutral, while C. vulgaris had slightly alkaline properties. Electrical conductivity differed markedly, with N. oculata showing the higher value (19,270 ±4.58 µS/cm), indicating a higher soluble salt content, consistent with the detection of NaCl and KCl as major crystalline phases by XRD. SEM–EDX analysis revealed diverse morphological features of the surface and the detection of several major elements. No detectable heavy metal signals were observed in the EDX spectra analyzed, although this does not confirm their absence. TGA/DTG and DSC allowed the identification of patterns of the decomposition of the sample and its phase changes, as well as FTIR, which confirmed the presence of functional groups corresponding to proteins, carbohydrates, lipids, and hydroxyl groups in the analyzed samples. In general, the results demonstrate distinct physicochemical and structural properties of the three biomasses and confirm their potential as soil amendments. However, their actual agronomic effectiveness and safety require further validation through soil and plant-based experiments and quantitative contaminant analyses.