Urban greeneries are at risk of declining soil organic carbon (SOC) stocks due to mal-management and human disturbance. However, only a few studies have assessed the quantity and quality of SOC in highly disturbed urban environments, which limits finding the best practices to augment SOC stability. In this study, we aimed to 1) investigate the SOC vulnerability in urban greeneries and compare it with natural grasslands and 2) elucidate the SOC vulnerability in relation to environmental variables and soil microbial activity. In natural grassland (GL), urban parks (UP), urban green strips (UGS), and urban roadside trees (URT), nine soil samples per each were collected (n = 36). We measured the SOC content of four different soil fractions: light fraction (LF), macro- and micro-aggregate occluded particulate organic matter (macroPOM and microPOM), and mineral-associated organic matter (MAOM). The SOC vulnerability was calculated by dividing the ‘LF+macroPOM’ by ‘microPOM+MAOM’. Subsequently, we analyzed soil bulk density (BD), pH, and microbial parameters including hydrolase and oxidase activities, basal respiration, and glomalin-related soil protein (GRSP). As a result, the highest SOC vulnerability was in the URT, followed by UGS, UP, and GL in the order. Specific enzyme activities (enzyme activity/SOC stock) and basal respiration were also greater in urban soil, particularly in URT. These results implied the current SOC stock in urban soil is continuously depleting. Furthermore, the GRSP content, which could help the aggregate formation, was significantly lower in the URT and UGS compared to the UP and GL. To explain how the relationship between environmental variables and microbial activity contributes to changes in SOC vulnerability, we performed structural equation modeling (SEM). The SEM result shows that higher soil pH increases oxidase activity, and a higher BD decreases GRSP. These changes lead to an upsurge in hydrolase activity, ultimately elevating the SOC vulnerability. Thus, it indicates that the relatively high pH and higher BD of urban soil increase the oxidase and hydrolase activities of microorganisms and continue to consume existing SOC. The insights gained from our study can contribute to developing adequate strategies to enhance SOC stability and sustainability of urban greeneries