Systems and methods for intelligent threat detection and prevention in point-of-sale terminals are disclosed. According to an embodiment, a method for intelligent threat detection and prevention in point-of-sale terminals may include: (1) receiving, by a backend computer program and from a threat collector agent executed on a point-of-sale terminal for a merchant, merchant behavioral activity involving a payment application executed by the point-of-sale terminal that was captured by the threat collector agent; (2) identifying, by the backend computer program, fraud or a threat from the merchant behavioral activity by providing the merchant behavioral activity to a trained merchant behavioral threat modeler; and (3) executing, by the backend computer program, a preventative action in response to the identified fraud or threat.