How did Eukaryotic cells originate? The endosymbiosis theory is how people think Eukaryotic cells originated. The endosymbiosis theory states that organelles such as mitochondria and chloroplasts originated when larger prokaryotes engulfed but did not digest smaller prokaryotes. Mutual benefits permitted this symbiotic relationship to be maintained, allowing the smaller cells to evolve into the eukaryotic organelles observed today.