Molecular beam epitaxy (MBE) is a powerful tool in modern technologies, including electronic, optoelectronic, spintronic, and sensoric applications. The primary factor determining epitaxial heterostructure properties is the growth mode and the resulting atomic structure and microstructure. In this paper, we present a novel method for growing epitaxial layers and nanostructures with specific and optimized structural and magnetic properties by assisting the MBE process using electromagnetic and mechanical external stimuli: an electric field (EF), a magnetic field (MF), and a strain field (SF). The transmission of the external fields to the sample is realized using a system of specialized sample holders, advanced transfers, and dedicated manipulators. Examples of applications include the influence of MFs on the growth and anisotropy of epitaxial magnetite and iron films, the use of EFs for in situ resistivity measurements, the realization of in situ magneto-optic measurements, and the application of SFs to the structural modification of metal films on mica.