Transcription of developmental genes is controlled by multiple enhancers. Frequently, more than one enhancer can activate transcription from the same promoter in the same cells. In these cases, how is regulatory information from multiple enhancers combined to determine the overall expression output of their shared promoter? To investigate this question, we quantified nascent transcription driven by a pair shadow enhancers, each individual of the pair, and their duplications in Drosophila embryos using live imaging. This set of constructs allows us to quantify the “computation” made by the pairs of enhancers: their combined output expression as a function of the expression that they drive separately. We show that the computation performed by these shadow enhancers and duplications varies across the expression pattern, implying that how their activities are combined depends on the transcriptional regulators bound to the enhancers in different parts of the embryo. Characterizing the computation made by multiple enhancers is a critical first step in developing conceptual and computational models of gene expression at the locus level, where multiple enhancers collaborate.