AbstractDuring the aircraft conceptual design phase, many different design options need to be explored and compared in a short time frame. To speed up this process, efforts have been made in the past decades to digitalize parts of the design process, with a focus on the automation of the repetitive and non‐creative tasks inherent to the iterative design process. Whilst many of the newly developed methodologies focus on specific parts of the design process, a holistic model‐based design framework, incorporating the latest design technology developments, is lacking. To fill this gap, this paper presents the latest version of the Design and Engineering Engine (DEE) framework, originally proposed in the early 2000s and progressively matured through the experience of several international research collaborations. The DEE enables the setup and execution of Multidisciplinary Design Analysis and Optimization (MDAO) problems for aircraft (sub)systems, leveraging the automated, rule‐based modeling capabilities offered by Knowledge‐Based Engineering (KBE) and recent developments in the automatic formulation and integration of MDAO workflows. While the traditional MDAO process focuses on a given product architecture, the DEE allows also architectural design studies and makes use of Model‐Based Systems Engineering (MBSE) principles to address the whole design process, from requirements modeling up to the automatic verification of the requirements. In practice, the DEE provides a single conceptual framework or template from which specific design framework instances can be formulated and executed, according to the user's needs. This paper describes the DEE architecture and its implementation concepts. Furthermore, it demonstrates the application of the DEE template to four different scenarios, ranging from a simple requirement verification study, up to the simultaneous synthesis and optimization of an aircraft system and its production process, including multiple system architecture options.