The success of engineering complex technical systems is determined by meeting customer requirements and institutional regulations. One example relevant to the automobile industry is the United Nations Economic Commission of Europe (UN ECE), which specifies the homologation of automobile series and requires proof of traceability. The required traceability can be achieved by modeling system artifacts and their relations in a consistent, seamless model—an effect-chain model. Currently, no in-depth methodology exists to support engineers in developing certification-compliant effect-chain models. For this purpose, a new methodology for certification-compliant effect-chain modeling was developed, which includes extensions of an existing method, suitable models, and tools to support engineers in the modeling process. For evaluation purposes, applicability is proven based on the experience of more than 300 workshops at an automotive OEM and an automotive supplier. The following case example is chosen to demonstrate applicability: the development of a window lifter that has to meet the demands of UN ECE Regulations R156 and R21. Results indicate multiple benefits in supporting engineers with the certification-compliant modeling of effect chains. Three benefits are goal-oriented modeling to reduce the necessary modeling capacity, increasing model quality by applying information quality criteria, and the potential to reduce costs through automatable effect-chain analyses for technical changes. Further, companies in the automotive and other industries will benefit from increased modeling capabilities that can be used for architecture modeling and to comply with other regulations such as ASPICE or ISO 26262.