Agricultural soils that are covered by vegetation, crop residue or snow are less susceptible to degradation processes such as erosion, organic matter depletion, structural decline and loss of fertility, and a high level of soil cover also maintains wildlife habitat, especially for soil micro-fauna. Agriculture Canada has developed a model which estimates the number of days in a year in which soil is covered under a variety of crop types, tillage practices and soil-landscape conditions. One “Soil Cover Day” (SCD) can be achieved with 100% cover for one day, 50% cover for 2 days, 10% cover for 10 days, and so on. The soil cover model includes tillage impacts, crop canopy development and harvesting of crop residue. Spatial estimates are based on area-weighting of all crop and tillage systems within the land unit. This study integrated the Soil Cover model with maps of land cover and soil quality in order to assess the impact of land use and management scenarios related to cellulosic ethanol production. Our analysis shows that harvesting crop residues up to approximately 20% by weight reduces soil cover by more than 1 day only in the low-yielding grassland regions of western Canada, while harvesting more than 40% reduces soil cover by more than 1 day over large areas of the country. Growing switchgrass on currently idle marginal land could produce about 80% of Canada’s current ethanol production, while simultaneously marginally increasing food production and improving soil quality. Increasing ethanol production beyond that level could encroach on current commodity production or require land clearing. Conversion of all annual crops currently grown on marginal land to perennial energy crops could increase Canadian ethanol production 8-fold and would increase the national average soil cover dramatically, from 282 to 289 days per year. However, conversion of marginal land to cellulosic crops represents a significant decline in the area of cereals, oilseeds and pulses, and intensification of production to compensate could virtually eliminate perennial crops on good soil and cause a significant decline in soil cover. Converting marginal land to switchgrass production and implementing a cropping system with 1/3 perennial crops and 2/3 annual crops on high-quality soils would provide the best soil cover situation of all scenarios tested, but the decline in area of annual crops could result in reduced food production and induce land clearing. Elimination of intensive tillage in favour of conservation tillage would improve soil quality, but would not reduce the pressure for intensification on prime soils. We conclude that from the perspective of food production and environmental sustainability, the best option for incorporating ethanol production into current production systems is to grow biomass crops on marginal land, while at the same time promoting further use of conservation tillage to offset the intensification of annual crop production on high-quality soil.