The aim of the study was to evaluate the effect of inclusion of micronized full-fat camelina, flax, or sunflower seeds in the diet for broiler chickens on the performance productivity, nutrient utilization, and composition of intestinal microbial populations and to assess the possibility of modification of the resistance of isolated bacteria to chemotherapeutic agents with different mechanisms of action. The use of micronized oilseeds improved the broiler chicken body weight (P = 0.035) and the FCR value (P = 0.045) in the final rearing stage by enhancement of the utilization of total protein and organic matter. Lactobacillus-Enterococcus spp., Bifidobacterium spp., Escherichia coli, and Salmonella spp. were isolated from small intestinal contents, and Enterobacteriaceae taxa were detected in the cecum and cloaca of the broiler chickens. The addition of micronized camelina seeds (CAM.IR) contributed to an increase in the Bifidobacterium counts in the small intestine, compared with the control treatment (P < 0.050). Escherichia coli bacteria were not isolated only in the CAM.IR treatment. Nitrofurantoin and chloramphenicol were the most effective agents against the isolates from the cecum and cloaca in all oilseed treatments, whereas streptomycin exhibited the lowest efficacy. In the CAM.IR and micronized sunflower seed (SUN.IR) treatments, there were higher counts of trimethoprim/sulfamethoxazole-resistant Enterobacteriaceae strains than in the control and micronized flax seed (FLA.IR) treatments (P < 0.05). There was a difference between strains isolated from the cecum and cloaca only in the FLA.IR treatment, i.e., increased tetracycline sensitivity was exhibited by strains isolated from the cloaca (13% vs. 50%), also in comparison with the control treatments (P = 0.054). In comparison with the CAM.IR and control treatments, reduced numbers of multi-resistant strains were found in the cloaca isolates from the for FLA.IR and SUN.IR variants. Micronized camelina, flax, and sunflower seeds can be used as part of an effective nutritional strategy focused on optimization of the efficiency of rearing broiler chickens, as they positively modify intestinal microbial populations and increase bacterial sensitivity to the analyzed chemotherapeutic agents.