The demand for non-cow milk and the products derived from it, is constantly increasing; thus, correct and effective pasteurization becomes necessary. Typical practices for evaluating milk pasteurization are mainly based on the thermal inactivation of an endogenous enzyme, alkaline phosphatase (ALP). The ALP tests, originally designed and applied to pasteurized cow milk, are often used to control pasteurization in non-cow milk, without sufficient data on their suitability; EFSA calls on the scientific world for collecting more information on the subject. In this study, the pertinent details of the ALP assay for non-cow milk products are summarized, and a comparison is performed regarding the evaluation of the adequacy of commercially available tests for the determination of ALP activity in non-cow milk. At the same time, raw and pasteurized non-cow milk was analyzed microbiologically using standard ISO methods and MALDI-TOF MS in order to confirm the thermal effect on common microorganisms. In these preliminary results, various ALP tests do not appear to be fully reliable as indicators for the pasteurization of some types of non-cow milk such as camel and donkey milk or even goat and sheep milk, using the EFSA proposed limits. ALP commercial kits may not be suitable as pasteurization indicators for various types on non-cow milk, and alternatives should be investigated.