The number of craft breweries and the volume of craft beer produced globally is growing exponentially. However, little is known about their differences with mainstream beers regarding mycotoxin profile, pesticide and pollutant residues and elemental composition. Given that beer is one of the most consumed beverages worldwide, it is important to shed light on its toxicological profile. In this study, samples of 23 craft beers and 19 mainstream Spanish beers were collected to perform a comparative analysis including 8 mycotoxins, 225 pesticide residues and 50 POPs, and 50 elements. Mycotoxins were not detected in craft beers, while 100% of mainstream beers presented at least one mycotoxin. In contrast, craft beers contained higher average pesticide residues than their mainstream counterparts, although significant differences were only found in Mepiquat and Metrafenone content. No persistent organic pollutants were detected in any sample. The elemental composition presented differences between the two groups both in the concentration of elements and their hierarchy. In conclusion, the toxicological profile of all beers was safe and is unlikely to constitute a hazard to consumer health. Craft beers present significant differences from their mainstream counterparts in all the dimensions explored.