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(1) Intestinal microbial parasites are major contributors to the global burden of gastrointestinal disease. Such infections are mainly caused by <i>Cryptosporidium</i>, <i>Giardia duodenalis</i>, and <i>Entamoeba histolytica</i>. These parasites are transmitted either directly or indirectly through oral–fecal routes. Previous reports suggested that camels could play a role in the zoonotic transmission of various clinically and veterinary important intestinal parasites, however, limited data are available on intestinal infections of camels, particularly on a molecular level. We aimed to explore the occurrence of these three parasites in camels (<i>Camelus dromedarius</i>) in Algeria. (2) A total of 68 samples—63 stool samples from camels and five from the environment—were collected from two desert regions in Algeria and analyzed using PCR and qPCR methods. (3) Overall, 7% of the camels tested positive for zoonotic subtypes of <i>Cryptosporidium</i> spp., while 16% of the camels tested positive for <i>G. duodenalis</i>. Two environmental samples also tested positive for <i>G. duodenalis</i>. None of the samples were positive for <i>Entamoeba histolytica</i>. (4) Our results provide one of the first molecular-based identification of these gut parasites in dromedary camels in Algeria. The presence of <i>G. duodenalis</i> in the host and the environment unveils, in part, the circulation route of this parasite. Our results will spearhead further investigations into the prevalence and epidemiology of gut parasites in hoofed animals and raise questions concerning their role in health and disease in the area.