While several studies have implicated polyamines (PAs) in development, little research has been done in genetically tractable model systems like Drosophila. Here, we integrate transcriptional and metabolic data across Drosophila development, and are the first to show temporal, stage-specific regulation of PA accumulation in embryonic trachea and eye discs using immunohistochemistry. Understanding the regulation driving this accumulation can provide insight into PA metabolism and transport. Our findings suggest that Drosophila has great potential for investigating PAs in developmental biology.