AlN nucleation layers are the basement of GaN-on-Si structures grown for light-emitting diodes, high frequency telecommunication and power switching systems. In this context, our work aims to understand the origin of propagation losses in GaN-on-Si High Electron Mobility Transistors at microwaves frequencies, which are critical for efficient devices and circuits. AlN/Si structures are grown by Metalorganic Vapor Phase Epitaxy. Acceptor dopant in-diffusion (Al and Ga) into the Si substrate is studied by Secondary Ion Mass Spectroscopy and is mainly located in the first 200 nm beneath the interface. In this region, an acceptor concentration of a few 1018cm-3 is estimated from Capacitance-Voltage (C-V) measurements while the volume hole concentration of several 1017 cm-3 is deduced from sheet resistance. Furthermore, the combination of scanning capacitance microscopy and scanning spreading resistance microscopy enables the 2D profiling of both the p-type conductive channel and the space charge region beneath the AlN/Si interface. We demonstrate that samples grown at lower temperature exhibit a p-doped conductive channel over a shallower depth which explains lower propagation losses in comparison with those synthesized at higher temperature. Our work highlights that this p-type channel can increase the propagation losses in the high-frequency devices but also that a memory effect associated with the previous sample growths with GaN can noticeably affect the physical properties in absence of proper reactor preparation. Hence, monitoring the acceptor dopant in-diffusion beneath the AlN/Si interface is crucial for achieving efficient GaN-on-Si microwave power devices.