Aluminum-germanium nanowires (NWs) thermal activated solid state reaction is a promising system as very sharp and well defined one dimensional contacts can be created between a metal and a semiconductor, that can become a quantum dot if the size becomes sufficiently small. In the search for high performance devices without variability, it is of high interest to allow deterministic fabrication of nanowire quantum dots, avoiding sample variability and obtaining atomic scale precision on the fabricated dot size. In this paper, we present a reliable fabrication process to produce sub-10 nm Ge quantum dots (QDs), using a combination of ex-situ thermal annealing via rapid thermal annealing (RTA) and in-situ Joule heating technique in a transmission electron microscope (TEM). First we present in-situ direct joule heating experiments showing how the heating electrode could be damaged due to the formation of Al crystals and voids at the vicinity of the metal/NW contact, likely related with electro-migration phenomena. We show that the contact quality can be preserved by including an additional ex-situ RTA step prior to the in-situ heating. The in-situ observations also show in real-time how the exchange reaction initiates simultaneously from several locations underneath the Al contact pad, and the Al crystal grows gradually inside the initial Ge NW with the growth interface along a Ge(111) lattice plane. Once the reaction front moves out from underneath the contact metal, two factors jeopardize an atomically accurate control of the Al/Ge reaction interface. We observed a local acceleration of the reaction interface due to the electron beam irradiation in the transmission electron microscope as well as the appearance of large jumps of the interface in unpassivated Ge wires while a smooth advancement of the reaction interface was observed in wires with an Al2O3 protecting shell on the surface. Carefully controlling all aspects of the exchange reaction, we demonstrate a fabrication process combining ex-situ and in-situ heating techniques to precisely control and produce axial Al/Ge/Al NW heterostructures with an ultra-short Ge segment down to 8 nanometers. Practically, the scaling down of Ge segment length is only limited by the microscope resolution.