The dynamics of organic C pools in constructed soils for urban farming, and how these pools interact with the mineral phase to form stable aggregates, may provide important information regarding their ability to store and sequester carbon. Technosols produced from concrete and excavation waste combined with wood chips, compost, and biochar (C + WCB and E + WCB, respectively), and an all-organic control treatment (WCB), were analyzed two years after the establishment of an urban milpa system. The size distribution and stability of aggregates, the distribution of C in aggregate size fractions, and the molecular composition of their organic and mineral phases were investigated. All treatments were mostly composed of macroaggregates (80–90% of the total aggregate size distribution), with 2–8% of microaggregates and a variation of 4–14% for the silt + clay fraction. Differential allocation of C in aggregate size fractions was observed when comparing C + WCB and E + WCB Technosols, while this element was more evenly distributed in the aggregate fractions of the WCB control treatment. The presence of recalcitrant and labile C compounds in silt + clay size fractions of C + WCB evidenced its heterogeneity in terms of C cycling potential. Moreover, the E + WCB showed a higher preservation of recalcitrant C compounds in microaggregates and silt + clay fractions. Thus, the proposed Technosols presented a significant potential to stabilize C in aggregate size fractions, and may contribute to long-term C storage while providing an on-site strategy for the final disposal of this type of urban waste.