The aerospace industry has set ambitious targets to meet environmental goals while under pressure to develop novel and optimized aircraft configurations effectively. Multidisciplinary Design Analysis and Optimization (MDAO) are increasingly used to optimize aircraft and their systems. Model-Based System Engineering (MBSE) methods show the potential to make the design process more effective, integrate new disciplines, and capture complex certification constraints. Today, MBSE and MDAO are not connected; different methods and tools are used, not harvesting the full potential of both approaches. This paper discusses the need for improved system architecting in the aircraft conceptual design process and introduces a framework to use MBSE in connection to MDAO. In this framework, the MBSE environment compiles system information within a system architecture specification, acting as the backbone and visual support for each stage in the systems architecting process. MDAO is used for the evaluation of system architectures. This paper presents a case study as part of the EU-funded AGILE4.0, in which the specific link between model specification in the MBSE tool Capella and a system-level MDAO workflow is explored. Overall, this paper presents a practical contribution to linking MBSE and MDAO and paves the way for better integration of MBSE into the aircraft design process, thereby enabling MBSE implementation from conceptual design onwards. Furthermore, this will enable more detailed system analysis, such as safety analysis, starting in conceptual design, based on architecture models.