Background: Kalahari truffle (Kalaharituber pfeilii) is found in the Kalahari desert and nearby regions (Africa). This study assessed the microbiological quality and safety, mycotoxins, and heavy metals contents of raw Kalahari truffle sold in Namibia. Methods: Batches of Kalahari truffles were purchased from informal markets and different vendors in Namibia. Total aerobic, coliform, yeast, and moulds counts, and Salmonella were assessed. Also, some mycotoxins and heavy metals were determined. Data were analyzed using SPSS Statistics Software, Version 25. Results: Total aerobic count of unwashed truffles ranged from 4.4 to 7.3 log Colony Forming Unit (CFU)/g. Total coliform counts detected in truffles were 6.0 log CFU/g. Salmonella was not detected. Doxynivalenol was the most prevalent mycotoxin. Fumonisin B1 levels ranged from 17.4 to 142.1 µg/kg. Ochratoxin A levels in unwashed truffles ranged from 0.1 to 48.5 µg/kg. Total aflatoxin levels were 26.3 to 27.5 µg/kg, while zearalenone levels ranged from 45.0 to 9,680 µg/kg. The iron content was up to 746.72 mg/kg. Cadmium and zinc were detected in the studied samples, but mercury and nickel were no detectable in any samples. Conclusion: The studied truffle samples were safe in terms of Salmonella, mercury, and nickel. However, some of the detected microorganisms, mycotoxins, and heavy metals in underprized Kalahari truffles may impair the safety, shelf life, and human health. Thus, they should be subjected to appropriate processing before consumption.