Biochar and biogas slurry have been proved to improve the quality of some soil types, but the long-term effects on fluvo-aquic soil are not fully understood. This study aimed to compare the continuity effects of peanut-shell biochar and biogas slurry on the physicochemical properties, microbial population size, and enzyme activities of fluvo-aquic soil. We conducted a four-year field experiment of winter wheat-summer maize rotation in the North China Plain. Along with equal nitrogen inputs, three treatments were applied—conventional fertilizers, peanut-shell biochar, and hoggery biogas slurry—after which various soil quality indicators were compared. Compared with those of control, both biochar and biogas slurry increased the soil total nitrogen and organic matter content, and improved soil aggregation, microbial biomass, and actinomycetes. Biogas slurry decreased soil pH and improved urease and protease activities. With biochar and biogas slurry treatments, wheat yield increased by 8.46% and 23.47%, and maize yield by 18% and 15.46%, respectively. Biogas slurry increased the content of crude protein and starch in the grains. Both biogas slurry and peanut-shell biochar improved fluvo-aquic soil nutrient content, water-stable macroaggregates, and microbial population, which might be related to their high nutrient content, large specific surface area, adsorption capacity, and functional groups. Biogas slurry generally exhibited stronger effects than biochar probably because of its richness in nutrients and bioactive substances.