This paper presents a certification-driven design process for an Unmanned Medium-Altitude- Long-Endurance (UAV MALE) air vehicle, including on-board system design and placements, electro-magnetic compatibility analysis, and thermal risk assessments. In literature, the preliminary aircraft design phase is mainly driven by mission performances and structural integrity aspects. However, the inclusion of other disciplines, like on-board system design or electro-magnetic compatibility, or thermal analysis, can lead to more efficient and cost- effective solutions and becomes paramount for non-conventional configurations like unmanned vehicles or highly electrified platforms. In the EC-funded AGILE 4.0 project (2019-2022), the traditional scope of the preliminary aircraft design is extended by including domains that are usually considered only in later design phases, such as certification, production and maintenance. In this paper, the AGILE 4.0 design environment supports the definition and execution of a certification-driven design process of a UAV MALE configuration, using a Model-Based Systems Engineering (MBSE) approach.