The disclosed embodiments describe cover detection systems, controllers, and aircraft. The aircraft includes the controller and parts of the cover detection systems. A cover detection system includes an engine, a first sensor, a second sensor, an engine cover, and a controller. The engine has moving parts and defines a fluid opening. The fluid opening exposes the moving parts to an ambient environment. The first sensor component is located proximate to the engine and the second sensor component is configured to interact with the first sensor component. The engine cover assembly includes an engine cover and a second sensor. The engine cover is configured to cover the fluid opening. The controller is configured to determine whether the engine cover is installed on the engine based on an interaction between the first sensor component and the second sensor component.