Ochratoxin A (OTA) in coffee is associated with serious health problems and significant economic loss. The state of Chiapas is the top coffee producer in Mexico, accounting for 41.3% of the national production, and the second largest organic coffee-producing area worldwide. Due to the lack of information about the OTA content in Chiapas coffee, 100 coffee samples from Chiapas were collected and classified according to their variety, type (roasted or nonroasted), processing and cultivation, in the 2017/2018 cycle. The average OTA concentration in 97 of the analyzed samples was 0.41 μg/kg. OTA was not detected in 52% of the samples; in 45% of the samples, the concentration ranged between 0.05 and 3.4 μg/kg, below the limit of European regulations (<5 μg/kg), and in only 3% of the samples did the OTA values exceed the European regulations. The statistical analysis revealed that the prevalence of OTA depends on the variety, type, and processing (p ≤ 0.05). No significant differences were observed between organic and conventionally cultivated coffee. In instant coffee (produced domestically), the average OTA concentration in 14 samples was 0.93 μg/kg. The probability of finding OTA in instant coffee is higher than that in Chiapas coffee. These results suggest that the prevalence of OTA in coffee from Chiapas is low and that it is less likely to be found in wet-processed, roasted, arabica coffee.