Natural products are increasingly attracting attention from both basic and applied science. Plant secondary metabolites, especially alkaloids, are receiving interest from a wide range of researchers due to their biological activity. They are produced to protect plants from diseases and herbivores. Therefore, they reveal a toxic activity that affects organisms at various levels of biological organization. A growing amount of research is proving their antimicrobial, antifungal, insecticidal, and anticancer activities. That makes them applicable in various fields from medicine, to pharmacology, veterinary, and toxicology, to crop protection. This Special Issue of Toxins, "Biological Activities of Alkaloids: From Toxicology to Pharmacology"", collects 15 manuscripts describing the ecological, biological, pharmacological, and toxicological effects as well as structural and analytical aspects of plant alkaloids, their mode of action, and possible application in veterinary, medicine, and plant protection. These studies prove the potential for alkaloid application in various areas of science.