Summary: We study the imprint that certain quantization ambiguities may leave in effective regimes of the hybrid loop quantum description of cosmological perturbations. More specifically, in the case of scalar perturbations we investigate how to reconstruct the Mukhanov-Sasaki field in the effective regime of loop quantum cosmology, taking as starting point for the quantization a canonical formulation in terms of other perturbative gauge invariants that possess different dynamics. This formulation of the quantum theory, in terms of variables other than the Mukhanov-Sasaki ones, is crucial to arrive at a quantum Hamiltonian with a good behavior, eluding the problems with ill defined Hamiltonian operators typical of quantum field theories. In the reconstruction of the Mukhanov-Sasaki field, we ask that the effective Mukhanov-Sasaki equations adopt a similar form and display the same Hamiltonian structure as the classical ones, a property that has been widely assumed in loop quantum cosmology studies over the last decade. This condition actually restricts the freedom inherent to certain quantization ambiguities. Once these ambiguities are removed, the reconstruction of the Mukhanov-Sasaki field naturally identifies a set of positive-frequency solutions to the effective equations, and hence a choice of initial conditions for the perturbations. Our analysis constitutes an important and necessary test of the robustness of standard effective descriptions in loop quantum cosmology, along with their observational predictions on the primordial power spectrum, taking into account that they should be the consequence of a more fundamental quantum theory with a well-defined Hamiltonian, in the spirit of Dirac’s long-standing ideas.