Technological progress, upcoming cyber-physical systems, and limited resources confront small and medium-sized enterprises (SMEs) with the challenge of complexity management in product development projects spanning over the entire product lifecycle. SMEs require a solution for documenting and analyzing the functional relationships between multiple domains such as products, software, and processes. The German research project FuPEP “Funktionsorientiertes Komplexitätsmanagement in allen Phasen der Produktentstehung” aims to address this issue by developing an assistance system that supports product developers by visualizing functional relationships. This paper presents the methodology and results of the assistance system’s requirements elicitation with two SMEs. Conducting the elicitation during a global pandemic, we discuss its application using specific techniques in light of COVID-19. We model problems and their effects regarding complexity management in product development in a system dynamics model. The most important requirements and use cases elicited are presented, and the requirements elicitation methodology and results are discussed. Additionally, we present a multilayer software architecture design of the assistance system. Our case study suggests a relationship between fear of a missing project focus among project participants and the restriction of requirements elicitation techniques to those possible via web conferencing tools.