Subsistence patterns during the Early Bronze Age I through the Iron Age II (3600-586 BCE) are the topic of many archaeobotanical and zooarchaeological studies. The results of these two disciplines are usually published separately, depriving us of an all-encompassing view of subsistence and agriculture during this time period since people did not solely make use of animal or plant products. In this paper, our goal is to integrate faunal and botanical lines of evidence and study developments in subsistence using multivariate statistics. By analysing individual and integrated datasets of botanical and faunal remains, we aim to better understand the role of diverse variables, such as chronology, mean annual precipitation, and elevation within the composition of our datasets. We see chronological differences, a distinction between sites at higher (400–600 mm) and lower (200–400 mm) precipitation ranges and differences between sites at different elevations (0–100 m and 500–600 m). We also highlight methodological issues intrinsic to differences in genesis and quantification of archaeobotanical and zooarchaeological datasets. We conclude that to obtain a complete understanding of subsistence during the Bronze and Iron Age in the Southern Levant, archaeobotanists and zooarchaeologists need to work on integrating their data on a site-specific level. This will allow us to obtain a holistic understanding of subsistence and agricultural practices on both a site and regional level and allow us to develop a stronger framework for understanding social and political developments that occurred during these time periods.