Antibiotics are active substances frequently used to treat and prevent diseases in animal husbandry. Most veterinary antibiotics are excreted after administration, in some cases up to 90% of the consumed dose can be found in the faeces and/or urine as parent compound. Livestock excrement is used around the world as natural fertilizers or, after processing, as organic fertilizers for crops and grasslands. Natural and organic fertilizers are an excellent source of nutrients for plants, but due to the presence of veterinary antibiotics in them, they may pose a threat to the natural environment, mainly to soil microorganisms, but also to human and animal health. Therefore, the work aimed to develop and validate an analytical method using the UHPLC-MS/MS technique and to analyze real samples of natural and organic fertilizers. Our research has shown that over 38% of natural fertilizers are contaminated with antibiotics, mainly doxycycline in concentrations reaching up to several dozen milligrams per kilogram of fertilizers. In the case of organic fertilizers that undergo processing, the presence of antibiotics was found in over 37% of the analyzed samples. The presented analytical method can be a tool for assessing the presence of veterinary antibiotics in solid natural and organic fertilizers.