Microalgae (MA) and purple phototrophic bacteria (PPB) have the ability to remove and recover nutrients from digestate (anaerobic digestion effluent) and pre-settled pig manure that can be Utilized as bio-fertilizer and organic fertilizer. The objective of this study was to compare the effectiveness of MA and PPB as organic fertilizers and soil conditioners in relation to plant growth and the soil biological processes involved in nitrogen (N) and carbon (C) cycling. To this end, a glasshouse experiment was conducted using MA and PPB as bio-fertilizers to grow a common pasture ryegrass (Lolium rigidum Gaudin) with two destructive harvests (45 and 60 days after emergence). To evaluate the rhizosphere bacterial community, we used barcoded PCR-amplified bacterial 16S rRNA genes for paired-end sequencing on the Illumina Mi-Seq. Additionally, we used phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis for the detection of putative functional genes associated with N and soil-C cycling. There was a significant increase in plant growth when the soil was amended with PPB, which almost performed as well as the chemical fertilizers. Analysis of the rhizosphere bacteria after the second harvest revealed a greater abundance of Firmicutes than in the first harvest. Members of this phylum have been identified as a biostimulant for plant growth. In contrast, the MA released nutrients more slowly and had a profound effect on N cycling by modulating N mineralization and N retention pathways. Thus, MA could be developed as a slow-release fertilizer with better N retention, which could improve crop performance and soil function, despite nutrient losses from leaching, runoff, and atmospheric emissions. These data indicate that biologically recovered nutrients from waste resources can be effective as a fertilizer, resulting in enhanced C- and N-cycling capacities in the rhizosphere.