We show that in the mathematical framework of the quantum theory, the classical pigeonhole principle can be violated more directly than previously suggested, i.e., in a setting closer to the traditional statement of the principle. We describe how the counterfactual reasoning of the paradox may be operationally grounded in the analysis of the tiny footprints left in the environment by the pigeons. After identifying the drawbacks of recent experiments of the quantum pigeonhole effect, we argue that a definitive experimental violation of the pigeonhole principle is still needed and propose such an implementation using modern quantum computing hardware: a superconducting circuit with transmon qubits