The objective of this study was to examine the effects of biochar compared to organic fertilizer on soil quality and microbial biomass as well as wheat yield in the saline-alkaline lands. A three-year field trial was conducted on moderately saline-alkaline land in the Yellow River Delta region (YRD) with six treatments: biochar (B1: 5 t, B2: 10 t, B3: 20 t ha− 1 year− 1) and organic fertilizer (OF1: 5 t, OF2: 7.5 t ha− 1 year− 1) as well as control (CK). The results showed that both biochar and organic fertilizer increased total organic carbon (TOC), total nitrogen (TN), NH4+-N, and NO3−-N, and reduced pH, thereby increasing soil microbial biomass carbon (MBC) and nitrogen (MBN), MBC/TOC ratio, and MBN/TN ratio, but organic fertilizer increased soil nutrients and microbial biomass better than biochar. Correlation analysis revealed that soil water content (SWC), soil salt content (SSC), and Na+ were the most important factors influencing wheat yield. When compared to CK, the SSC and Na+ decreased by 5.55–7.52% and 3.86–9.39%, respectively, and SWC increased by 5.14–5.62% in the biochar treatment, while they increased by 1.07–10.19%, 1.08–7.58%, and 2.96–3.84% in the organic fertilizer treatment, respectively. Accordingly, wheat yield in biochar treatment was 0.90–14.20% higher than organic fertilizer treatment (4.49–4.80 t ha− 1). Collectively, B2 had the lowest SSC and Na+ and the highest yield, as well as efficiently increasing soil nutrients and microbial biomass, suggesting that it may be a better agricultural practice for improving soil quality and increasing wheat yield in the YRD.