Meat and fish are muscle foods rich in valuable nutrients, such as high-quality proteins, vitamins, and minerals, and, in the case of fish, also unsaturated fatty acids. The escalation of meat and fish production has increased the occurrence of pesticide and antibiotic residues, as result of pest control on feed crops, and antibiotics used to fight infections in animals. Meat and fish are usually cooked to enrich taste, soften texture, increase safety, and improve nutrient digestibility. However, the impact of cooking on nutritional properties and formation of deleterious compounds must be understood. This review summarizes studies, published in the last decade, that have focused on how domestic cooking affects: (i) composition of nutrients (protein, fatty acids, vitamins, and minerals); (ii) antibiotic and pesticide residue contents; and (iii) the formation of cooking-induced contaminants (heterocyclic aromatic amines, polycyclic aromatic hydrocarbons, and thermal degradation products of antibiotics and pesticides). Cooking affects the nutritional composition of meat and fish; frying is the cooking method that causes the greatest impact. Cooking may reduce the pesticide and antibiotic residues present in contaminated raw meat and fish; however, it may result in the formation of degradation products of unknown identity and toxicity. Control of cooking time and temperature, use of antioxidant-rich marinades, and avoiding the dripping of fat during charcoal grilling can reduce the formation of cooking-induced contaminants.