Over the past few decades, use of nanostructures has become widely popular in the different field of science. Nanoparticles, in particular, are situated between the molecular level and bulk matter size. This size range gave rise to a wide variety physical phenomena that are still not quite understood. Magnetic nanoparticles are at their hype due to their applications in medical field, as a catalyst in a wide number of chemical reactions, in addition to their use for information storage devices and spintronics. In this work, we are interested in studying the intrinsic magnetic properties (magnetic moments and anisotropy) of FeCo nanoparticles. Thus, in order to completely understand their properties, mass-selected FeCo nanoparticles were prepared using the MS-LECBD (Mass Selected Low Energy Cluster Beam Deposition) technique in the sizes range of 2-6 nm and in − situ embedded in a matrix in order to separate them, to avoid coalescence during the annealing and to protect during transfer in air. From a first time, the structural properties (size, morphology, composition, crystallographic structure) of these nanopar- ticles were investigated in order to directly correlate the modification of the magnetic properties to the structure and chemical ordering of the nanoparticles after high temperature treatment. In addition to the bimetallic FeCo nanoparticles, reference Fe and Co systems were also fabricated and studied using the same techniques. The structural properties were investigated using high resolution transmission electron microscopy (HRTEM), anomalous x-ray diffraction (AXD) and extended x-ray absorption fine structure (EXAFS) where a phase transition from a disordered A2 phase to a chemically ordered CsCl B2 phase was observed and further validated from the magnetic findings using SQUID magnetometry and x-ray magnetic circular dichroism (XMCD)