Alternative cropping systems are gaining attention throughout the world in order to increase the sustainability of agro-ecosystems. On the Canadian prairies, the tillage-based crop-fallow system has been replaced by no-till reduced input systems or tillage-based organic systems with more diversity in crop rotations but with no external inputs. However, the long-term effects of these alternative systems on weed and yield parameters have not been assessed. A study to examine weed and crop yield dynamics under diverse cropping systems was conducted within a 18-year cropping systems study near Scott, Saskatchewan. The trial was laid out in a split-split-plot design with four replicates. The main plots were three levels of inputs; a high input system (HIGH) that used tillage and inputs to maximize yield, a reduced system (RED) that used no-till practices and minimal inputs, and a tillage-based organic system (ORG) with no external inputs. The subplots were cropping diversity (rotations); fallow-annual grains (LOW), diversified annual grains (DAG), and diversified annuals and perennial forage (DAP). The sub-sub plots were the six phases of each rotation. There was an input by rotation interaction for weed biomass but not for weed density and crop yields. ORG systems had 7× and 4× greater weed density (107 plants m−2), 4× higher weed biomass (154kgha−1), and 32% and 35% lower yields (1052kgha−1) than RED and HIGH systems respectively. RED and HIGH input systems had similar crop yields and lower weed density than ORG. The LOW rotation had the lowest weed density. LOW and DAG rotations had similar yields, which were higher than in DAP. All systems showed an increase in weed density and biomass over time but did not impact on crop yields which was increasing over time likely influenced by a concurrent increase in rainfall. This study concludes that eliminating tillage and reducing agrochemicals is possible but eliminating agrochemicals requires better crop rotations for weed management as well as for nutrient management.