Embodiments are directed to securing mixed-mode applications in a semi-trusted environment. In an embodiment, a computer system securely loads native data files associated with a mixed-mode application. The secure loading ensures that the native components upon which the managed component depends are authentic. The computer system implements a securely stored handle associated with the loaded native data files to provide secure communications between the managed component and the loaded native data files. The handle provides a trusted function pointer to an associated mixed-mode application function. The computer system also initiates a security permission request for each resource that is passed to the native components during execution of the mixed-mode application, so that each resource is verified before execution.