Decision-based attacks construct adversarial examples against a machine learning (ML) model by making only hard-label queries. These attacks have mainly been applied directly to standalone neural networks. However, in practice, ML models are just one component of a larger learning system. We find that by adding a single preprocessor in front of a classifier, state-of-the-art query-based attacks are up to 7$\times$ less effective at attacking a prediction pipeline than at attacking the model alone. We explain this discrepancy by the fact that most preprocessors introduce some notion of invariance to the input space. Hence, attacks that are unaware of this invariance inevitably waste a large number of queries to re-discover or overcome it. We, therefore, develop techniques to (i) reverse-engineer the preprocessor and then (ii) use this extracted information to attack the end-to-end system. Our preprocessors extraction method requires only a few hundred queries, and our preprocessor-aware attacks recover the same efficacy as when attacking the model alone. The code can be found at https://github.com/google-research/preprocessor-aware-black-box-attack.