Cyclophosphamide (CP) is a potent anticancer agent widely used to treat various malignancies and autoimmune diseases after organ transplantation. However, its therapeutic benefits are often accompanied by severe toxicity, primarily attributable to oxidative stress. In contrast, Moroccan honey, including varieties, such as thyme and thistle, is known for its multifaceted medicinal properties, including potent antioxidant activity. This study sought to investigate the protective potential of Moroccan honey against CP-induced genotoxic and cytotoxic effects in mouse bone marrow cells. The results revealed a significant increase in genotoxicity and cytotoxicity following CP administration (20 mg/kg), as evidenced by elevated micronuclei frequency and a reduced ratio of polychromatic to normochromatic erythrocytes. However, pretreatment with Moroccan honey (1 g/kg) for a duration of 6 days effectively attenuated these adverse effects. Furthermore, biochemical analysis demonstrated that mice receiving honey exhibited notable improvements in liver function, as indicated by decreased levels of alanine aminotransferase, aspartate aminotransferase, and uric acid. Histological examination revealed reduced hepatic damage characterized by diminished steatosis, apoptosis, necrosis, and inflammatory cell infiltration. These findings underscore the potential of thyme and thistle honeys, as a promising adjunctive therapy to mitigate the deleterious effects associated with CP treatment, offering potential applications in complementary chemotherapeutic strategies.