Many embedded system applications involve storing and querying large datasets. Existing research in this area has focused on adapting and applying conventional database algorithms to embedded devices. Algorithms designed for processing queries on embedded devices must be able to execute given the small amount of available memory and energy constraints. In this paper, the authors describe the Flash MinSort external sorting algorithm that uses an index, generated at runtime, to take advantage of fast random reads in flash memory. This algorithm adapts to the amount of memory available and performs best in applications where sort keys are clustered. Experimental results show that Flash MinSort is two to ten times faster than previous approaches for small memory sizes where external merge sort is not executable.