A method of flight management and guidance of an aircraft executed by a flight management system FMS comprises the steps of: generating a reference trajectory, generating a short-term trajectory, periodically transmitting the short-term trajectory, generating a long-term trajectory, formatting the segments of the long-term trajectory, periodically transmitting the long-term trajectory, storing the long-term trajectory transmitted, testing the validity of the FMS sub-assembly, when the FMS sub-assembly is valid: identifying, by the autonomous guidance module, the active segment of the short-term trajectory, generating, by the autonomous guidance module, a first flight guidance order on the basis of the active segment of the short-term trajectory; when the FMS sub-assembly is not valid: identifying, by the autonomous guidance module, the active segment of the stored trajectory, generating, by the autonomous guidance module, a second flight guidance order on the basis of the active segment of the stored trajectory.