This chapter explores the structural constraints and physiological mechanisms that enable symbiotic associations among prokaryotes to develop into physiologically integrated organisations. Specifically, it investigates the conditions that facilitate the transformation of endosymbionts into organelles, as exemplified by the evolution of mitochondria and plastids. The chapter argues that biofilms and bacterial endosymbiosis exhibit diverse spatial organisations that impose unique constraints on their constituent organisms, thereby providing distinct mechanisms of collective control. These spatial organisations confer a specific type of stability over time and open up various evolutionary pathways for converting a collective association into an integrated individual. By elucidating key physiological dimensions of functional integration, this chapter contributes to a more precise definition of “functionally integrated individuality”.