Electrically manipulating the quantum properties of nano-objects, such as atoms or molecules, is typically done using scanning tunnelling microscopes and lateral junctions. The resulting nanotransport path is well established in these model devices. Societal applications require transposing this knowledge to nano-objects embedded within vertical solid-state junctions, which can advantageously harness spintronics to address these quantum properties thanks to ferromagnetic electrodes and high-quality interfaces. The challenge here is to ascertain the devices effective, buried nanotransport path, and to electrically involve these nano-objects in this path by shrinking the device area from the macro- to the nano-scale while maintaining high structural/chemical quality across the heterostructure. Weve developed a low-tech, resist- and solvent-free technological process that can craft nanopillar devices from entire in-situ grown heterostructures, and use it to study magnetotransport between two Fe and Co ferromagnetic electrodes across a functional magnetic CoPc molecular layer. We observe how spin-flip transport across CoPc molecular spin chains promotes a specific magnetoresistance effect, and alters the nanojunctions magnetism through spintronic anisotropy. In the process, we identify three magnetic units along the effective nanotransport path thanks to a macrospin model of magnetotransport. Our work elegantly connects the until now loosely associated concepts of spin-flip spectroscopy, magnetic exchange bias and magnetotransport due to molecular spin chains, within a solid-state device. We notably measure a 5.9meV energy threshold for magnetic decoupling between the Fe layers buried atoms and those in contact with the CoPc layer forming the so-called spinterface. This provides a first insight into the experimental energetics of this promising low-power information encoding unit.