Reducing agricultural runoff is important year round, particularly on landscapes that receive wintertime applications of manure. No-tillage systems are typically associated with reduced runoff loads during the growing season, but surface roughness from fall tillage may aid infiltration on frozen soils by providing surface depressional storage. The timing of winter manure applications may also affect runoff, depending on snow and soil frost conditions. Therefore, the objective of this study was to evaluate runoff and nutrient loads during the freezing season from combinations of tillage and manure application timings. Six management treatments were tested in south-central Wisconsin during the winters of 2015–2016 and 2016–2017 with a complete factorial design: two tillage treatments (fall chisel plow vs. no-tillage) and three manure application timings (early December, late January, and unmanured). Nutrient loads from winter manure application were lower on chisel-plowed versus untilled soils during both monitoring years. Loads were also lower from manure applied to soils with less frost development. Wintertime manure applications pose a risk of surface nutrient losses, but fall tillage and timing applications to thawed soils can help reduce loads.