In organic production systems, composted manure and a short-term grass/legume sod rotation component may improve soil health. However, little is known about the lasting benefits of these two management practices for the duration of the several crop components of an organic rotation. This study was designed to determine whether 3 years of grass sod and composted manure application affected soil properties and crop biomass yield at the beginning and end of 4 years of organic crop production. The effects of the sod rotation component and composted manure on bulk density (BD), dry (dryGMD [dry aggregate geometric mean diameter]) and wet (wetGMD [wet aggregate geometric mean diameter]) aggregation, soil organic matter, bioavailable nutrient concentrations, and crop biomass were determined in two long-term rotations at the West Virginia University Certified Organic Research Farm in Morgantown, West Virginia. The rotations were a 4-year continuous rotation of corn (Zea mays L.), soybean (Glycine max L. Merr.), wheat (Triticum aestivum L.), and kale/cowpea (Brassica oleracea)/Vigna unguiculata L. Walp.), and a 7-year rotation of the same crop sequence followed by 3 years of grass/legume (orchardgrass/red clover, Dactylis glomerata L./Trifolium pretense L.) sod. Two composted manure levels, 0 (nonmanured [n-M]) and 2.25 (manured [M]) Mg ha−1, were imposed only to the corn and wheat rotation components. Results for 2013 and 2014 showed that manure application significantly improved soil physical and chemical properties for corn and kale/cowpea regardless of the sod component. In the corn component, BD was lower (P < 0.0001) in M soils (1.13 Mg m−3) than in n-M soils (1.24 Mg m−3). A significant (P = 0.0060) decrease in BD due to the sod component was observed when corn was not manured, 1.27 and 1.21 Mg m−3 in the 4- and 7-year rotations, respectively. Soil organic matter was significantly (P < 0.0001) higher in M than n-M soils and was also higher for the rotation with the sod component, regardless of manure application (P < 0.0001). The sod component resulted in significantly (P = 0.012) increased pH in n-M soils (5.61 and 5.89 for the 4- and 7-year rotations, respectively). Soil health and corn biomass were found to be most improved in soils receiving manure and subject to sod insertion in the rotation. The soil organic matter, dryGMD, wetGMD, and bioavailable soil P and Mg were found to be higher in M soils under corn in the 7-year rotation. Although differences in soil health indicators were measured in kale/cowpea soils, no differences (P = 0.510) in the biomass indicator were observed. This research supports the use of manure, in conjunction with insertion of a short-term grass/legume sod component, to improve soil health in organic crop rotations.