Magnaporthe oryzae, the pathogen responsible for the rice blast disease, produces a specialised infection structure called an appressorium that uses massive turgor to break the tough outer cuticle of the rice leaf. Appressorium development is a tightly regulated process that requires surface recognition of a hard hydrophobic surface, successful traversal of cell cycle checkpoints, and autophagic conidial cell death. It is however unknown how organelle trafficking is regulated and spatially controlled in parallel with autophagy and cell cycle progression. I developed molecular markers and a quantitative technique to monitor the trafficking of specific organelles in M. oryzae wild-type strain Guy11 and an ∆atg8 autophagic mutant. Live-cell imaging and quantitative analysis enabled us to characterise the regulated trafficking of 10 organelles within the three-celled conidium during appressorium development. High-resolution live-cell imaging using a photoactivatable green fluorescent protein indicates that germination establishes a separate developmental programme for each conidium cell, permitting organelle trafficking from a single conidium cell into the appressorium while targeting the remaining two cells for autophagy. We discovered that organelle trafficking occurs independently of cell cycle checkpoints for transport into the appressorium. I have quantified the temporal sequence of organelle movement and de novo organelle biogenesis in the incipient appressorium using photoconvertible fluorescent localisation microscopy. Our study shed light on the spatial control of organelle dynamics associated with fungal infection-related morphogenesis.