Most agroecosystems receive inputs of anthropogenically derived nutrients, which impact soil organic carbon (SOC). However, the impact of the combination of different fertilizer types, as well as of various amounts of nitrogen (N), phosphorus (P), and potassium (K) fertilization, on SOC remains to be determined. Here, we reviewed 212 published studies to identify the consequences of different types and levels of N, P, and K fertilization on SOC across northern hemisphere cropland soils. The average effect size of fertilization on SOC was 0.2707 ± 0.0086 (95% confidence interval: 0.2539–0.2875, p < 0.0001). Categorical variable analysis revealed that the fertilization type significantly influenced the effect size in mineral plus organic fertilization > pure organic fertilization > pure mineral fertilization. The increased available nutrients led to the retention of organic C from farmyard manure or crop straw and limited nutrient loss, increasing C sequestration. Intermediate N (100–300 kg ha−1 year−1) and K (50–150 kg ha−1 year−1) application with high P (>60 kg ha−1 year−1) fertilization produced the most significant effect on the SOC stocks. Heterogeneity analysis revealed that the annual average precipitation, annual average temperature, water conditions, and tillage type significantly affected the average effect size. Overall, the meta-analysis revealed that multi-nutrient fertilization, with intermediate N and K levels and a high P level, decreased the dependency of the organisms released from SOM decomposition and had strong positive effects on increasing SOC in agroecosystems.