Virtually all current major social and environmental challenges such as financial crises, migration, the erosion of democratic institutions, and the loss of biodiversity involve complex systems comprising decision-making, interacting, adaptive agents. To understand how such agent-based complex systems function and respond to change and disturbances, agent-based modeling (ABM) is increasingly recognized as the main way forward. Many motivating examples of agent-based models exist that are realistic enough to successfully support the management of complex systems, but these solutions are case-specific and contribute few general insights into the functioning of systems. General theory, though, is highly needed because we cannot model each system and question. Still, across disciplines, a critical mass of expertise has accumulated that could transform ABM into a more coherent and efficient approach to discover the functioning of complex social-economic-ecological systems. To this end, we need a cross-disciplinary discussion among researchers and a goal-oriented synthesis to identify the general principles and theories essential to improve our understanding and management of complex systems.