Online pharmacies are popular worldwide. In Germany, there were 150 active online pharmacies in 2022. As the competition is therefore fierce and new customers need to be acquired, some of these online pharmacies create catalogues that advertise products in self-medication to attract the interest of potential customers. This study analyzed the allergy, cold, and gastrointestinal tract categories from the summer/spring 2023 catalogues of two different online pharmacies in Germany. A comparison of the active ingredients in both catalogues and an analysis of the product’s conformity with the German AWMF (Association of the Scientific Medical Societies in Germany) guidelines as well as international guidelines were carried out. In medicine, guidelines serve as evidence-based decision-making aids tools to ensure adequate patient care. The online catalogue of online pharmacy 1 showed conformity of 65% with AWMF guidelines, and the online catalogue of online pharmacy 2 showed conformity of 59% with AWMF guidelines. The online catalogue of online pharmacy 1 showed conformity of 44% with international guidelines, and the online catalogue of online pharmacy 2 showed conformity of just only 17% with international guidelines. Thus, there is a substantial lack of conformity of online pharmacy self-medication catalogues with national and international guidelines. For several indication areas including market-relevant rhinosinusitis and irritable bowel syndrome, consensus between AWMF and international guidelines was poor. The lack of evidence-based presentation of online pharmacy catalogues constitutes a risk for consumer safety. This risk must be assessed in future studies, for example by studies on intoxications caused by self-medication that is non-compliant with guidelines. Our results also underline the necessity of a stricter surveillance of the German self-medication market.