Crop rotation promotes productivity, nutrient cycling, and effective pest management. However, in row-crop systems, rotation is frequently limited to two crops. Adding a third crop, especially a perennial crop, might increase crop-rotation benefits, but concerns about disruption of agricultural and ecological processes preclude grower adoption of a three-crop rotation. The objective of the present research was to determine whether weed seed banks differ between a sod-based rotation (bahiagrass–bahiagrass–peanut–cotton) and a conventional peanut–cotton rotation (peanut–cotton–cotton) and the importance of crop phase in weed seed-bank dynamics in a long-term experiment initiated in 1999 in Florida. Extractable (ESB) and germinable (GSB) seed banks were evaluated at the end of each crop phase in 2012 and 2013, and total weed seed or seedling number, Shannon-Weiner's diversity (H′), richness, and evenness were determined. ESB increased in H′ (36%), richness (29%), and total number of weed seeds (40%) for sod-based compared with conventional rotation, whereas GSB increased 32% in H′, 27% in richness, and 177% in total number of weed seedlings. Crop phase was a determinant factor in the differences between crop rotations. The first year of bahiagrass (B1) exhibited increases in weed seed and seedling number, H′, and richness and had the highest values observed in the sod-based rotation. These increases were transient, and in the second year of bahiagrass (B2), weed numbers and H′ decreased and reached levels equivalent to those in the conventional peanut–cotton rotation. The B1 phase increased the germinable fraction of the seed bank, compared with the other crop phases, but not the total number of weed seeds as determined by ESB. The increases in H′ and richness in bahiagrass phases were mainly due to grass weed species. However, these grass weed species were not associated with peanut and cotton phases of the sod-based rotation. The results of the present study demonstrated that including bahiagrass as a third crop in a peanut–cotton rotation could increase weed community diversity, mainly by favoring increases in richness and diversity, but the structure and characteristics of the rotation would prevent continuous increases in the weed seed bank that could affect the peanut and cotton phases.