Livestock farming occupies 57% of agricultural area in France and has contrasting impacts on the environment. Studies have analyzed relations between livestock farming and soil organic carbon (SOC) content, but the influence of livestock farming on soils is difficult to perceive at a large scale. The objective of this study was to increase understanding of impacts of livestock farming on soils that receive livestock manure depending on different initial levels of SOC content, at cantonal level. To this end, we used French soil and agricultural databases to analyze relations between livestock farming practices and SOC content. We used statistical data calculated from the French soil test database for the periods 2000–2004 and 2010–2014. For livestock farming practices, we used data from the French agricultural census of 2000 and 2010, and for spreading of livestock manure, data from the French program to control pollution of agricultural origin (2002–2007) and data from the French Livestock Institute. The novelty of our large-scale analysis is to differentiate the origin of livestock manure (herbivore or granivore) and the type of crop on which it was spread (crops or grasslands). Statistical analysis was performed at the cantonal scale for France using the method of generalized least squares. We show for the first time that, at the national scale, spreading of livestock manure influences SOC content and dynamics significantly. Our results also show the importance of the nature of the manure; solid manure increases SOC content, unlike liquid manure. Spreading herbivore manure on crops increases SOC content, but spreading granivore manure may decrease it. Livestock manure spread on grasslands has no significant effect on SOC content, possibly due to under-representation of grassland soils in the soil database. These results demonstrate the importance of the complementary between crop and livestock to maintain soil ecosystem services, including soil fertility.