Under intensive low residue agricultural systems, such as those involving potato ( L.)-based systems, stagnant crop yields and declining soil health and environmental quality are common issues. This study evaluated the effects of pen-pack cow () manure application (20 Mg·ha) and cover crops on nitrate dynamics and soil N supply capacity, subsequent potato yield, selected soil properties, and soil-borne disease. Eight cover crops were tested and included grasses, legumes, or a mixture of legumes and grasses, with red clover ( L.) used as a control. Forage pearl millet ( L.) was associated with highest dry matter. On average, red clover had 88% higher total N accumulation than the treatments mixing grasses and legumes, and the former was associated with higher soil nitrate in fall before residue incorporation and overwinter, but this was not translated into increased potato yields. Pearl millet and sorghum sudangrass ( × var. Sudanese) were associated with lower soil nitrate in comparison to red clover while being associated with higher total potato yield and lower numerical value of root-lesion nematodes (), although this was not statistically significant at 5% probability level. Manure incorporation increased total and marketable yield by 28% and 26%, respectively, and increased soil N supply capacity by an average of 44%. Carbon dioxide released after a short incubation as a proxy of soil microbial respiration increased by an average of 27% with manure application. Our study quantified the positive effect of manure application and high-residue cover crops on soil quality and potato yield for the province of Prince Edward Island.