Dormancy is a general microbial life-history trait that leads to the emergence of seed banks across diverse ecosystems. While the primary forces driving seed banks include macroscale factors like resource supply, the importance of microscale factors such as individual encounters with resource molecules are often overlooked. Here, we used >10,000 individual based models (IBMs) to simulate energetic, physiological, and ecological processes across combinations of resource-, spatial-, and trophic-complexity. We found that increasing rates of encounter of individual organisms with resource molecules led to greater abundance, greater productivity, and larger seed banks. We also found that the chemical complexity of resource molecules reduced encounter rates, which led to increased variability in the size of seed banks. Encounter-driven ‘boom and bust’ dynamics also caused resource-rich environments to simultaneously host large seed banks and serve as hotbeds of microbial activity. In conclusion, microscale phenomena appear to be essential for understanding the emergence of seed banks, the energetic basis of microbial life history trade-offs, and variation in the abundance and activity of microbial communities.