Antarctic krill (Euphausia superba) and its products have garnered increasing attention as valuable natural resources because of their rich nutritional profile, particularly that of their bioactive compounds such as proteins and phospholipids. These components offer significant health benefits, including antioxidant and anti-inflammatory properties, which have attracted consumers seeking nutritional supplements and functional foods. However, the safety and quality of Antarctic krill products are of critical concern, especially concerning the presence of elements such as arsenic (As) and fluoride (F) and the potential allergenic properties of krill proteins. This review provides a comprehensive analysis of the safety issues surrounding Antarctic krill and its products, addressing key concerns such as the presence of As, F, and allergenic proteins, and strategies to mitigate these risks. One of the primary food safety concerns of Antarctic krill is its potential to accumulate As through its diet of plankton and algae. Various forms of As exist in the natural environment; their toxicity depends on the chemical form. Inorganic arsenic, particularly arsenite (As(Ⅲ)) and arsenate (As(Ⅴ)), is highly toxic, whereas organic arsenic compounds, such as arsenobetaine (AsB), are considered nontoxic or of low toxicity. Studies have shown that Antarctic krill contain As primarily in the less harmful organic forms, with AsB accounting for a significant proportion of the total As content. The levels of inorganic As in Antarctic krill and its products are typically far below the regulatory limits set by food safety standards, such as the national standard of China (GB 2762-2022), which stipulates that the maximum allowable inorganic As content in aquatic products should not exceed 0.50 mg/kg. However, some krill oil samples exceeded the specific standard of 0.1 mg/kg for inorganic As in krill oil, highlighting the need for continued monitoring and control of As levels in these products. Another contaminant of concern in Antarctic krill is F; it naturally accumulates in marine organisms, particularly in the exoskeletons of crustaceans such as krill. Although F is an essential micronutrient at low concentrations, excessive F intake can lead to health issues such as skeletal fluorosis. Research has demonstrated that Antarctic krill and its products, especially krill meal and krill powder, contain elevated F levels because of the exoskeleton’s high F content. The presence of F limits the use of krill products in health supplements, but removing F remains a technical challenge. Current strategies for defluorination include physical and chemical treatments, such as enzymatic hydrolysis, calcium salt precipitation, and filtration. However, further research is required to improve the efficacy of these methods without compromising the nutritional quality of the products. The allergenic potential of Antarctic krill also poses a significant food safety issue. Krill contains proteins (e.g., tropomyosin) that are known allergens that can trigger immune responses in sensitive individuals, particularly those with shellfish allergies. Symptoms of krill protein allergies include skin reactions, respiratory issues, and gastrointestinal discomfort. Although there are no specific treatments for food allergies, several studies have explored methods to reduce the allergenicity of krill proteins. Techniques such as microwave treatment, ultrahigh-pressure processing, protease digestion, and electron beam irradiation have shown promising results in reducing the allergenic potential of tropomyosin and other proteins. For example, microwave and ultra-high-pressure treatments have been shown to reduce shrimp allergenicity, and protease digestion eliminates allergenic protein bands. Moreover, the Maillard reaction, commonly used in food processing, reduces the allergenicity of tropomyosin by altering its secondary structure. These findings offer potential solutions for rendering krill products safer for consumption by individuals with shellfish allergies. Given the growing demand for krill products in the food and nutraceutical markets, ensuring their safety and quality is essential. Future research should focus on understanding the mechanisms involved in As, F, and allergenic protein toxicity, developing more efficient methods for removing these harmful substances. Advances in processing technologies, such as improved defluorination techniques and novel methods for reducing protein allergenicity, are critical for enhancing the safety of krill products. In addition, regulatory frameworks must be strengthened to ensure that krill products meet food safety standards. This includes the use of advanced detection technologies for monitoring contaminants such as As and F and implementing strict labeling requirements for allergens. International cooperation is vital for sharing research findings and regulatory experiences, which can lead to the establishment of unified safety standards for krill products. Public education is another important aspect of ensuring consumer safety. Increasing awareness of the potential risks associated with krill consumption, including heavy metal contamination and allergenicity, can help consumers make informed decisions. Finally, ongoing policy development and establishing a comprehensive quality control system are crucial for protecting consumer health and ensuring the sustainable development of the Antarctic krill industry. In conclusion, Antarctic krill has immense potential as a sustainable and nutritious resource. However, ensuring the safety of its products is paramount. Through continued research, technological advancement, regulatory oversight, and public education, the krill industry can address safety concerns while meeting the growing consumer demand for healthy and functional foods.