A computer-implemented method for increasing security on computing systems that launch application containers may include (1) authenticating an application container that facilitates launching at least one application on a host computing system by verifying that the application container meets a certain trustworthiness threshold, (2) intercepting, via a policy-enforcement proxy, a command to perform a deployment action on the host computing system in connection with the authenticated application container, (3) determining that the deployment action potentially violates a security policy applied to the authenticated application container, and then in response to determining that the deployment action potentially violates the security policy, (4) modifying, via the policy-enforcement proxy, the command to prevent the potential violation of the security policy. Various other methods, systems, and computer-readable media are also disclosed.