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ABSTRACT Biological complexity is widely seen as the central, intractable challenge of engineering biology. Yet this challenge has been constructed through the field’s dominant metaphors. Alternative ways of thinking—latent in progressive experimental approaches, but rarely articulated as such—could instead position complexity as engineering biology’s greatest resource. We outline how assumptions about engineered microorganisms have been built into the field, carried by entrenched metaphors, even as contemporary methods move beyond them. We suggest that alternative metaphors would better align engineering biology’s conceptual infrastructure with the field’s move away from conventionally engineering-inspired methods toward biology-centric ones. Innovating new conceptual frameworks would also enable better aligning scientific work with higher-level conversations about that work. Such innovation—thinking about how engineering microbes might be more like user-centered design than like programming a computer or building a car—could highlight complexity as a resource to leverage, not a problem to erase or negate.