Soil organic carbon (SOC) management is key for soil fertility and for mitigation and adaptation to climate change, particularly in desertification-prone areas such as Mediterranean croplands. Industrialization and global change processes affect SOC dynamics in multiple, often opposing, ways. Here we present a detailed SOC balance in Spanish cropland from 1900 to 2008, as a model of a Mediterranean, industrialized agriculture. Net Primary Productivity (NPP) and soil C inputs were estimated based on yield and management data. Changes in SOC stocks were modeled using HSOC, a simple model with one inert and two active C pools, which combines RothC model parameters with humification coefficients. Crop yields increased by 227% during the studied period, but total C exported from the agroecosystem only increased by 73%, total NPP by 30%, and soil C inputs by 20%. There was a continued decline in SOC during the 20th century, and cropland SOC levels in 2008 were 17% below their 1933 peak. SOC trends were driven by historical changes in land uses, management practices and climate. Cropland expansion was the main driver of SOC loss until mid-20th century, followed by the decline in soil C inputs during the fast agricultural industrialization starting in the 1950s, which reduced harvest indices and weed biomass production, particularly in woody cropping systems. C inputs started recovering in the 1980s, mainly through increasing crop residue return. The upward trend in SOC mineralization rates was an increasingly important driver of SOC losses, triggered by irrigation expansion, soil cover loss and climate change-driven temperature rise.