We assessed the long-term application effects of slurry composting bio-filtration (SCB) liquid fertilizer on red pepper (Capsicum annuum L.) yield and soil response. Our study used a randomized complete block design with three replicates over five years (2007 to 2011). We evaluated seven nitrogen treatments: control, five rates of SCB (SCB0, SCB1, SCB2, SCB3, and SCB4), and chemical fertilizer (Urea3). SCB was used as basal fertilization and three top dressing doses of urea at the 30th, 60th, and 90th day after transplanting were applied. For plant analysis, fresh fruit yield, N uptake, fruit N use efficiency (FNUE), and quality (soluble sugar and capsaicinoid concentrations) were measured; and soil pH, electrical conductivity (EC), soil organic matter, inorganic N, P, exchangeable K, Ca, Mg, and Na, Zn, Fe, and Cu were analyzed. In this study, fresh fruit yield for Urea3 was similar to SCB3 and SCB4. Fruit soluble sugar and capsaicinoid concentrations were the same for all N treatments. The lowest FNUE was shown under SCB0 and the highest FNUE was under SCB4. Five years of SCB treatment had no effect on soil chemical properties. For example, soil pH, EC, and soil organic matter content did not show any changes for all N treatments, regardless of N fertilizer source, and soil P was not influenced by increasing SCB rates. Also, the concentrations of Fe, Mn, Zn, and Cu did not show any difference among treatments. Although the concentrations of K and Na in soil increased with SCB rate, the concentration of K was still less than the recommended K level from the National Academy of Agricultural Science, and the sodium adsorption ratio indicated that the increased Na may not adversely affect growing crops. Therefore, the accumulation of K and Na was not critical during our study. These results suggest that SCB for basal fertilization can be used as one of the N fertilizer sources, replacing chemical N fertilizer sources. The recommended SCB rate for basal fertilization should be 103 kg N/ha (SCB3) or 128 kg N/ha (SCB4). Consequently, use of SCB liquid fertilizer could provide an alternative source of pre-transplant N fertilizer for red pepper production.