This study aimed at evaluating the incidence of aflatoxin B1 (AFB1) and ochratoxin A (OTA) in thyme and thyme-based products, related dietary exposure, and cancer risk for regular and high consumption. A total of 160 samples were collected, and 32 composite samples were analyzed. AFB1 and OTA were respectively found in 84% (27/32) and 38% (12/32) of the samples. AFB1 exceeded the limits in 41% (13/32) and 25% (8/32) of the samples according to the Lebanese and European standards, respectively. OTA was unacceptable in only 6% (2/32) and 3% (1/32) of the samples according to the Lebanese and European standards, respectively. AFB1 and OTA daily exposure was shown to be 4.270 and 1.345 ng/kg bw/day, respectively. AFB1 was shown to be associated with 0.41 and 0.35 additional cancer cases per 100,000 persons per year for regular consumption, respectively; while for high consumption, an increase of 0.911 and 0.639 cancer cases per 100,000 person per year was noted, respectively. The margin of exposure (MOE) for OTA was >10,000 for the non-neoplastic effect and >200 for the neoplastic effect, representing no toxicological concerns for consumers.