Although various studies have investigated biochar (BC) soil amendments for improving soil microbial abundance, functions, and community structure, a comparison of dairy manure biochar (MBC) to wood biochar (WBC) is warranted given the large volume of manure produced in high-intensity dairy production. Additionally, the synergistic effects of different BC sources and loading percentages on microbial functions and community composition using massively parallel 16S DNA sequencing in BC-amended soils with different types of crops are limited. In this study, the synergistic effects of BC type, BC loading percentage, and crop types on soil fertility, prokaryote community diversity, and functions were investigated in a greenhouse study. The MBC and WBC were used to amend sandy loam soils at increasing BC loading percentages (0, 5, and 10%) to grow the cool-season forages crimson clover (Trifolium incarnatum; an annual legume) and Italian ryegrass (Lolium multiflorum Lam.; an annual forage grass) for 120 days. High nutrient concentrations in MBC shifted microbial communities towards r-strategists and alkaliphiles, potentially increasing the rate of nutrient bioremediation from high nitrogen- and phosphorus-containing soil amendments. This study enables emerging biochar agronomic use recommendations with different crops.