The apple cultivar, known for its adaptability and diverse varieties, has been extensively utilized for cider production, particularly in climatically suitable regions. Cider, an age-old alcoholic beverage derived from fermenting apple juice, is gaining popularity, especially among younger generations. Despite this trend, comprehensive knowledge regarding the toxicological profile of ciders remains limited, leaving room for potential chemical contaminants from raw ingredients or production methods. To address this gap, we conducted an unprecedented study analyzing sixty-eight cider samples from the Spanish market, encompassing both traditional ciders and newly developed apple-based flavored drinks referred to as “ciders.” Our investigation focused on pesticide residues, elemental profiles, and mycotoxin residues. In a groundbreaking approach, our study integrated the analysis of 225 pesticide residues, 50 Persistent Organic Pollutants (POPs), 11 mycotoxins (AFB1, AFB2, AFG1, AFG2, DON, FB1, FB2, H-2, HT-2, OTA, PAT, and ZEN), and a total of 50 elements. Pesticide residues were identified using GCMSMS and LCMSMS, elemental composition determined via ICPMS, and mycotoxins analyzed using LCMSMS. The significance of our research lies in addressing the dearth of toxicological analyses of ciders, despite their burgeoning global consumption and production. For pesticide residues and elemental composition, our results underwent statistical processing, revealing distinct differences between the elemental profiles of traditional ciders and “ciders.” Additionally, disparities were observed between cider and other low-alcohol fermented beverages like wines and beers. Concentrations of most pesticide residues and elements in the cider samples were deemed non-toxic, falling below allowable limits established by international organizations for other beverages such as water or wine. However, certain elements, notably Br and Pb in traditional ciders, raised potential concerns. Our findings underscore the necessity of establishing regulatory limits for pesticide residues, potentially hazardous elements, and mycotoxins in cider, a regulatory framework currently lacking on a global scale.