Plants contain diverse microorganisms that interact with their hosts and with each other. Beneficial bacteria can be utilised on crops to protect plants against biotic and abiotic stresses and to stimulate plant growth. However, the behaviour of specific microorganisms on and within plants is still underexplored. Knowledge of bacterial colonisation behaviour and the precise ecological niches in a natural environment of a target strain can lead to better application and utilisation of these microorganisms for crop enhancement, in different plant soil environments, and for both biocontrol and biofertilisation approaches in organic and integrated protection systems. Understanding colonisation characteristics will also provide information on putative new strategies for maximising inoculation efficiency and thus crop enhancement. In this chapter, we set out how beneficial bacteria can colonise their host plants under various conditions and demonstrate how an understanding of plant colonisation can be used to improve bacterial application approaches.