Modeling complex, nonlinear ecosystem processes across different timescales presents a significant challenge. We identify two key issues: selecting a representative timestep that captures interconnected processes across various timescales, and simulating these processes in an appropriate sequence. By synthesizing existing ecosystem frameworks, we find shared compromises between biological realism and computational performance. For the representative timestep, these include ‘selective elimination of timescales’, ‘biting the bullet’, ‘each in their own time’, and ‘capture the unseen’. For processing order, we identify hierarchical, logical, iterative, and random approaches. Similar challenges exist in other disciplines, and we show how transferring methods from multiple fields, along with smarter computing, can improve timescale integration. Overcoming these challenges requires innovative transdisciplinary solutions, and we outline directions for future research.