Crohn’s disease (CD) is a chronic inflammatory condition of the gastrointestinal tract. This case–control study included 20 patients with CD and 20 healthy controls at Mohammed VI University Hospital in Marrakech. The study aimed to characterize cultivable gut bacterial populations using culture-based methods and the Shannon index and to evaluate the in vitro antimicrobial activity of two Thymus essential oils. Patients were slightly older than controls and were more frequently sedentary, while dietary patterns were similar between the groups. Patients showed higher counts of Escherichia coli, Citrobacter spp., Klebsiella spp., and Enterococcus spp., together with lower Lactobacillus counts. The Shannon index showed a negative correlation with lifestyle score (Spearman’s ρ = −0.735, p = 0.049), while a positive correlation was observed with C-reactive protein levels (Spearman’s ρ = 0.574, p = 0.008). GC/MS analysis identified 30 compounds in T. leptobotrys essential oil and 33 in T. vulgaris essential oil, with carvacrol (87.48%) and thymol (76.41%) as the predominant constituents, respectively. Both essential oils produced inhibition zones against the bacterial strains tested; however, the selectivity index used in this study should be considered an exploratory metric. These findings provide preliminary in vitro evidence of antimicrobial activity and should be further investigated using standardized antimicrobial susceptibility methods and more comprehensive microbiota profiling. Larger studies combining culture-based and sequencing-based approaches are warranted.