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Sustainable crop production requires nutrient inputs to replace what was removed or lost. Replenishing nutrients using fertilizers and animal wastes is one of the most common input practices. While there is considerable research evaluating the efficacy of fertilizer and manure-based inputs for crop performance, nutrient use efficiency, and the subsequent impact to the environment, the influence of these inputs on soil health properties is less understood. The goals of this review are to summarize the state of literature on the influence of chemical fertilizer and manure-based inputs on soil health and to identify research gaps to refine efforts toward improved soil health, sustainability, and soil carbon storage. Conclusions suggest that chemical fertilizer inputs can increase soil organic matter and soil health provided that additions are not beyond what a plant can utilize. Manure-based inputs contribute to soil organic carbon and associated metrics; however, direct comparison of products is difficult as they are generally applied on a nutrient basis rather than carbon basis, which differentially affects their influence on soil health. Overall, nutrient-containing inputs show beneficial influences on soil health metrics; however, more focused research into their influence on soil health is needed.