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Background: Wastewater from sewage treatment plants contains high levels of nutrients, which can be used for plant nutrition. Classical wastewater treatment plants use complex microbial consortia of autotrophic and heterotrophic microorganisms for biological wastewater treatment. Certain autotrophic microalgae (e.g., species of the genera Chlorella, Scenedesmus, and Pediastrum) accumulate nutrients from wastewater very effectively. Aims: We investigated the potential of microalgae biomass obtained from a prototype wastewater treatment plant as a source of nutrients for crops, focusing on nitrogen. Methods: We provided wheat plants with different levels of algae biomass equivalent to 60, 120, and 180 kg N per hectare or with mineral fertilizer (N, P, and K) equivalent to the amounts contained in the algal biomass. Physiological and phenotypic traits were measured during growth, including vegetation indices, photosynthetic performance, growth, and nitrogen use efficiency (NUE). In addition, the adundances of Bacteria, Archaea and fungi and genes of ammonium oxidizing Bacteria and Archaea were determined in the rhizosphere of differently fertilized plants. Results: Microalgal application at fertilizer levels of 120 and 180 kg N ha–1 showed significantly improved physiological performance, growth, yield and nutrient uptake compared to the unfertilized control. Nevertheless, their yields and NUE were lower than with the application of equal amounts of mineral fertilization, while the adundance of rhizosphere microbes and ammonia‐oxidizing microorganisms were not significantly affected. Conclusions: Microalgae from wastewater treatments form a suitable source of organic fertilizer for wheat plants with only moderate reductions in N use efficiency compared to mineral fertilizer. [ABSTRACT FROM AUTHOR]