Purpose Free amino acids (FAAs) and peptides, and dissolved organic nitrogen (DON) comprise key pools in terrestrial soil carbon (C) and nitrogen (N) cycles. A comparative study of organic and conventional arable farming systems was conducted in Shanghai, China to determine the influence of management practices on characterization of AA and peptide dynamics. Materials and methods Soils from an accredited organic farm (OS), transitional farm (TS), and neighboring conventionally managed farm (CS) were sampled from agricultural areas in Shanghai, China, and the AA and peptide behavior of top soils were evaluated by 14C labeled techniques. Results and discussion Results showed that organic management resulted in significant increases (P < 0.05) in AA and peptide rate acquisition, possibly due to higher soil organic C (SOC) and soil respiration in OS, compared to TS and CS. The half-life of valine (Val), valine-proline-proline (Val-Pro-Pro), glutamate (Glu), and glutamate-phenylalanine (Glu-Phe) averaged across the three soils (OS, TS, and CS) was 10.6 ± 2.3, 9.4 ± 2.2, 7.1 ± 1.9, and 6.7 ± 1.5 h, respectively. The relative AA and peptide C amounts partitioned into respiration (15–32% of total) versus biomass production (68–85% of total C) was also affected by management strategy and generally followed the order CS>TS>OS; OS was significantly different from TS and CS; however, a significant difference was not detected between TS and CS. We hypothesize that AA and peptide mineralization acts as a purely biological process, as CHCl3 fumigation and autoclaving resulted in no observable mineralization. Results showed that AA and peptide addition to soil resulted in rapid N mineralization and subsequent NO −3–N production, which followed a progression based on soil N mineralization rate of OS>TS>CS. AAs and peptides were only weakly sorbed onto the soil solid phase; however, our results suggested that this did not limit soil bioavailability. Conclusions The results of our study indicated that soil management regimes have a substantial effect on AA and peptide behavior (mineralization, microbial uptake, and sorption, among other attributes) in horticultural production systems. Therefore, we propose that SOC and total microbial activity are likely key determinants governing AA and peptide behavior in horticultural soils.