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Amphibians, as the most threatened group of vertebrates, are the focus of investigation of various agents that could affect their fitness and survival. In this context, we examined the effects of naturally occurring bacteria and their combinations on the embryonic and larval development of common toad tadpoles (Bufo bufo). One egg string that was collected from the wild was disinfected in the lab and divided into short strings, each containing 20 eggs. These strings were exposed to three different control treatments, i.e., a sterile FETAX solution, water collected from the tadpoles’ native habitat, and sterilized habitat water, as well as to three different bacterial cultures isolated from habitat water (Bacillus sp., Mesobacillus sp.). We analyzed several morphometric variables (snout–vent length, total length, and weight), the energy budget by measuring body composition (proteins, carbohydrates, and lipids), and biomarker activity (acetylcholinesterase and lactate dehydrogenase). Our results indicate that the native microbial community had a negative effect on egg and tadpole development, as sterilized habitat water supported their highest development. Additionally, when grown in FETAX, pure bacterial cultures and their combinations decreased acetylcholinesterase activity but positively affected both tadpole size and energy budget. These findings suggest that bacteria can influence the larval development of common toads by modifying physiological traits. Future research should identify which microbes have beneficial or detrimental effects on amphibian development. Full article