Growth throughout the body responds to a multitude of environmental conditions, generating variation in body and organ size in accordance with the developmental environment. For animals, this poses a particular challenge; animals need to coordinate the development of their organs to ensure that irrespective of plasticity in organ and body size, organ patterning remains robust to maintain correct organ function. We explore the genetic mechanisms that coordinate plastic versus robust developmental processes across a range of environmental and physiological conditions using the fruit fly, Drosophila melanogaster. To understand how the body coordinates its development with that of its organs, we devised a staging scheme for the developing wing disc. Using the changes in expression of three patterning genes in the wing, Achaete, Senseless and Dachshund, we correlated the progression of patterning in the wing with whole body developmental events in altered environmental and physiological conditions. We have found that the wing aligns its development at specific developmental milestones, at the moult to the third instar and at pupariation, but the progression of wing disc pattern varies significantly between these milestones. Next, we determined the role of the steroid hormone ecdysone, known to regulate moulting and metamorphosis, in regulating the progression of pattern and the growth of the wing disc. By ablating the gland that produces ecdysone, we have found that the progression of Achaete, Senseless and Dachshund patterns differ in their requirement for ecdysone. Furthermore, we find that Senseless, but not Achaete or Dachshund, shows evidence of a disc size threshold for patterning to progress. Taken together, these data provide valuable insight into how developmental processes are coordinated across the body and how organs coordinate both plastic and robust processes throughout development.