Pen and paper-based value stream mapping (VSM) is the established tool for recording processes, identifying waste and deriving recommendations for action. However, today, its application in manufacturing industry requires a high level of effort and is challenging due to product and process complexity, as well as dynamics. To overcome these shortcomings, we are developing a methodology to apply process mining (PM) to internal logistics for a mixed-model assembly line. The methodology combines multidimensional process mining (MDPM) techniques with proven principles of lean production and VSM. Firstly, internal logistics is modelled using existing event data by automatically mapping physical logistics activities (e.g. transport, store). Secondly, to enable PM, the event data is transformed into enriched event logs. Thirdly, the MDPM approach contains (1) a discovery analysis, (2) a performance analysis and (3) a conformance analysis including a reference process classification for each individual part and process. Finally, a waste analysis and strategy for practitioners is designed to identify and prioritise wasteful parts and processes. The methodology has been applied and evaluated in a case study at a German automotive manufacturer. In the case study, we analysed 7500 parts and 15 reference processes. An analysis for each individual part and process has not been available yet. We could both identify part-specific root causes (e.g. a long lead time) and process-specific root causes (e.g. a low trace fitness). The main contribution of this paper is to provide an MDPM methodology for practitioners to enable a continuous recording, evaluation and waste analysis of each individual part and process within internal logistics.