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Abstract Boson Sampling is a computational paradigm representing one of the most viable and pursued approaches to demonstrate the regime of quantum advantage. Recent results have shown significant technological leaps in single-photon generation and detection, leading to progressively larger instances of Boson Sampling experiments in different photonic systems. However, a crucial requirement for a fully-fledged platform solving this problem is the capability of implementing large-scale interferometers, that must simultaneously exhibit low losses, high degree of reconfigurability and the realization of arbitrary transformations. In this work, we move a step forward in this direction by demonstrating the adoption of a compact and reconfigurable 3D-integrated platform for photonic Boson Sampling. We perform 3- and 4-photon experiments by using such platform, showing the possibility of programming the circuit to implement a large number of unitary transformations. These results show that such compact and highly-reconfigurable layout can be scaled up to experiments with larger number of photons and modes, and can provide a viable direction for hybrid computing with photonic processors.