Background: Knowledge of the responses of soil aggregates to various fertilization practices can contribute to sustainable soil management in urban vegetable agriculture. Aims: The study assessed the soil fertility, dry aggregate stability, and aggregate total carbon (TC) and nitrogen (TN) retention after the reapplication of biochar, and organic/inorganic fertilizers. Methods: Four replicates of ecological sanitation (ECOSAN) manure, NPK fertilizer, corncob biochar (CCB), and CCB, combined with urea and cattle manure (UCF), were established in a randomized complete block design. Results: The application of ECOSAN increased the soil pH and also resulted in significant accumulation of available phosphorus (P), calcium (Ca), and magnesium (Mg). Compared to CCB treatment, UCF + CCB produced significant increases in the TC, TN, P, Ca, and Mg concentrations by 53, 140, 227, 27, and 78%, respectively, and additionally increased the 4.75–2.00 mm large macroaggregates and mean weight diameter. The total carbon increased significantly in microaggregates (>0.25 mm); macroaggregates (4.75–0.25 mm); and in the micro- and macroaggregate fractions of the ECOSAN, CCB, and UCF + CCB treatments, respectively. More so, the TN in micro- and macroaggregates was increased maximally by UCF + CCB and minimally by the CCB treatment. Conclusions: The reapplication of CCB had limited potential for carbon sequestration in soil aggregates, but its combination with UCF better reflects carbon and nitrogen stabilization in micro- and macro- aggregates, with greater potential in large macroaggregates.