<p><strong>Background:</strong> Pre-Hispanic agroecosystems in Mexico City have changed the kind of crops, management practices, tools, and inputs, seriously impacting their biocultural value and sustainability. Previous studies have demonstrated these changes' economic, cultural, and political consequences. However, their effects on biodiversity have not been considered. The present study characterized the management carried out in three agroecosystems in the southeastern area of Mexico City and its possible relationship with agrobiodiversity. <strong>Objective</strong>: To evaluate the contribution of diversity, abundance, and composition of weeds as components of the sustainability of agroecosystems in Milpa Alta, Tláhuac, and Xochimilco municipalities. <strong>Methodology: </strong>179 interviews were conducted with campesinos. Weeds sampling in 30 plots, recording the abundance and frequency of each species. These data were used to estimate different ecological parameters. Information on management practices was transformed to develop an “agroecosystem sustainability index.” A multivariate analysis was applied to compare weed attributes between agroecosystems and spaces and to detect possible relationships between the index and ecological parameters. <strong>Results:</strong> 156 species were recorded. The <em>slope</em> had the highest diversity, and <em>ciénega</em> had the lowest. More than half of the weeds were native, and the <em>slope</em> exhibited the highest number. The Importance Value indicated no dominant species on the <em>slope, </em>opposite to<em> chinampa and ciénega</em>. Species composition also differed between the three agroecosystems. <em>Chinampa</em> was impacted the most, whereas the <em>slope</em> was least affected. <strong>Implications:</strong> The displacement of traditional crops and agricultural practices and the incorporation of technological practices have modified the ecological attributes of weeds, like their abundance and composition. <strong>Conclusion:</strong> Starting from the argument that ecological attributes of weeds can be used as an indicator of sustainability, the <em>slope</em> resulted in the agroecosystem being most sustainable and should be used as a model to recover the agrobiodiversity of <em>ciénegas</em> and <em>chinampas</em>. </p>