In this article, we operationalized a sustainability framing based on the Sustainable Rural Livelihood Resources Framework (SLF), which consists of five capitals—human, physical, social, financial, and natural. We proposed a sustainability index (SI) for two landscapes dominated by two agricultural systems: cattle ranching and small-scale family agriculture. Farm variables within each capital were analyzed using confirmatory factor analysis. Key variables were identified and index values were calculated for each capital. These were combined through a set of simultaneous equations to estimate farm-specific capitals and SI from the observed farm variables. Principal component and cluster analyses were used to group the farms according to their index scores and to further compare their characteristics. Furthermore, with the purpose of comparing the index scoring with an independent metric, a landscape indicator, which comes from a continuous forest, was calculated. From the results, the capitals that contributed to a higher SI score the most were financial and physical. As cattle ranching was associated with higher economic returns and infrastructure investments, this livelihood was identified as the most sustainable. Yet, cattle ranching has been a deforestation driver in the region. These results are attributed to the current conceptual framework design, which gives greater weight to material and economic variables; therefore, it generates a weak sustainability measure. Although the framework allowed us to identify land-use alternatives that could improve SI scores (i.e., silvopastoral systems), corrections to the proposed framework and methodological approach will need to include additional environmental benefits currently unaccounted for. Farmers that use their farms for conservation purposes should be recognized and compensated. An improved environmentally focused SI operational framework could help to endorse and promote sustainable livelihoods and to generate a strong sustainability measure.