These days, a growing consumer demand and scientific interest can be observed for nutraceuticals of natural origin, including apiculture products. Due to the growing emphasis on environmental protection, extensive research has been conducted on the pesticide and heavy metal contamination of bee products; however, less attention is devoted on other food safety aspects. In our review, scientific information on the less-researched food safety hazards of honey, bee bread, royal jelly, propolis, and beeswax are summarized. Bee products originating from certain plants may inherently contain phytotoxins, like pyrrolizidine alkaloids, tropane alkaloids, matrine alkaloids, grayanotoxins, gelsemium alkaloids, or tutin. Several case studies evidence that bee products can induce allergic responses to sensitive individuals, varying from mild to severe symptoms, including the potentially lethal anaphylaxis. Exposure to high temperature or long storage may lead to the formation of the potentially toxic 5-hydroxymethylfurfural. Persistent organic pollutants, radionuclides, and microplastics can potentially be transferred to bee products from contaminated environmental sources. And lastly, inappropriate beekeeping practices can lead to the contamination of beekeeping products with harmful microorganisms and mycotoxins. Our review demonstrates the necessity of applying good beekeeping practices in order to protect honeybees and consumers of their products. An important aim of our work is to identify key knowledge gaps regarding the food safety of apiculture products.