This study addresses the need for a comprehensive understanding of digestate and biochar in mitigating climate change and improving soil health, crucial for sustainable agriculture within the circular bioeconomy framework. Through a mesocosm experiment, soil was amended with digestates from pilot-scale reactors and two concentrations of biochar produced by pyrolysis of digested sewage sludge and waste wood. The Germination Index (GI) assay assessed phytotoxicity on Lactuca sativa and Triticum aestivum seeds. Greenhouse gas emissions (CO2, CH4, N2O) measurements, soil characteristics analyses, and the study of microbial community structure enriched the study\u2019s depth. The GI assay revealed diverse responses among by-products, dilution rates, and plant types, highlighting the potential phyto-stimulatory effects of digestate and biochar water-extracts. While digestate proved to be effective as fertilizer, concerns arose regarding microbial contamination. Biochar application reduced Clostridiaceae presence in soil but unexpectedly increased N2O emissions at higher concentrations, emphasizing the need for further research on biochar\u2019s role in mitigating microbial impacts. CO2 emissions increased with digestate application but decreased with a 10% biochar concentration, aligning with control levels. CH4 uptake decreased with digestate and high biochar concentrations. The study underscores the importance of tailored approaches considering biochar composition and dosage to optimize soil greenhouse gas fluxes and microbial communities.