We construct Hermitian representations of Lie algebroids and associated unitary representations of Lie groupoids by a geometric quantization procedure. For this purpose, we introduce a new notion of Hamiltonian Lie algebroid actions. The first step of our procedure consists of the construction of a prequantization line bundle. Next, we discuss a version of Kähler quantization suitable for this setting. We proceed by defining a Marsden–Weinstein quotient for our setting and prove a "quantization commutes with reduction" theorem. We explain how our geometric quantization procedure relates to a possible orbit method for Lie groupoids. Our theory encompasses the geometric quantization of symplectic manifolds, Hamiltonian Lie algebra actions, actions of bundles of Lie groups, and foliations, as well as some general constructions from differential geometry.