Industrial hemp (Cannabis sativa L.) derivatives are emerging as functional ingredients in companion animal nutrition; however, their long-term effects on the canine gut microbiome remain unclear. This exploratory study investigated the impact of dietary supplementation with two hempseed-based formulations (fiber-rich by-product vs. fat-rich oil coating) on the fecal microbiota of healthy adult dogs over 90 days. Twenty-four dogs were randomly assigned to control, hempseed by-product (11% inclusion), or hempseed oil (2% coating) diet groups. Fecal samples collected on days 0, 30, and 90 were analyzed using 16S rRNA gene sequencing to assess microbial composition and diversity. The hempseed oil group showed a distinguishable increase in species richness. Both hempseed-based diets were associated with compositional shifts in formulation-specific ways: the oil coating with a higher relative abundance of Lactobacillaceae (notably Ligilactobacillus), and the by-product with a higher relative abundance of Actinobacteriota (particularly Collinsella). Both treatments preserved several microbiota genera. Beta diversity analysis revealed significant temporal restructuring, with convergence toward a stabilized ecosystem by day 90. These findings demonstrate that hempseed fractions modulate the canine microbiome in a formulation-specific manner without disrupting ecological stability, supporting beneficial health effects in canine nutrition.