As the global food system contributes significantly to global greenhouse gas (GHG) emissions, understanding the sources of GHG emissions embodied in different components of food systems is important. The collapse of the Soviet Union triggered a massive restructuring of the domestic food systems, namely declining consumption of animal products, cropland abandonment, and a major restructuring of agricultural trade. However, how these complex changes have affected global GHG emissions is uncertain. Here, we quantified the net GHG emissions associated with changes in the former Soviet Union’s food systems. Changes in food production, consumption, and trade together resulted in a net emissions reduction of 7.61 Gt carbon dioxide equivalents from 1992 to 2011. For comparison, this corresponds to one quarter of the CO2 emissions from deforestation in Latin America from 1991 to 2011. The key drivers of the emissions reductions were the decreasing beef consumption in the 1990s, increasing beef imports after 2000, mainly from South America, and carbon sequestration in soils on abandoned cropland. Ongoing transformations of the food systems in the former Soviet Union, however, suggest emissions will likely rebound. The results highlight the importance of considering agricultural production, land-use change, trade, and consumption when assessing countries emissions portfolios. Moreover, we demonstrated how emissions reductions that originate from a reduction in the extent and intensity of agricultural production can be compromised by increasing emissions embodied in rising imports of agricultural commodities.