The quality of the embedding potential describing the environment surrounding a central quantum subsystem is crucial to provide accurate results in embedding calculations. In the fragment-based PE approach, a classical embedding akin to QM/MM, the environment is modeled using multipoles and polarizabilities that have been calculated explicitly for the fragments that make up the environment. The MFCC procedure is used to fragment large molecules such as proteins and nucleic acids. However, hydrogen bonds have not been considered in the MFCC procedure so far, despite their crucial role in many molecular structures, such as hydrogen-bonding solvents, proteins, and nucleic acids. In this work, we investigated the effect of incorporating hydrogen bonds in the MFCC procedure (MFCC(HB)) for deriving fragment-based multipoles and polarizabilities of environments of water solvents and proteins. Our analysis shows that including hydrogen bonds substantially improves the electrostatic potentials, and thus the multipoles and polarizabilities, of water clusters, α-helices, and β-sheets. To quantify the impact on the properties of a central quantum subsystem, we calculated the embedding potential on the vdW surface of a series of molecules in aqueous solution and of the chromophores in C1C2 and GFP. The improvement, calculated as an RMSD, ranged between roughly 10-60 kJ/mol, showing that there is potentially a large effect that can critically affect the calculated properties of the quantum subsystem. Indeed, the dipole moments of the quantum subsystems were reduced or increased by up to 0.9, while the effects on excitation energies, oscillator strengths, TPA cross-sections were modest.