In amorphous superconductors, superconducting and vortex pinning properties are strongly linked to the absence of long range order. Consequently, superconductivity and vortex phases can be studied to probe the underlying microstructure and order of the material. This is done here from resistance and local magnetization measurements in the superconducting state of FexNi1−xZr2 metallic glasses with 0 ≤ x ≤ 0.6. Firstly, we present typical superconducting properties such as the critical temperature and fields and their dependence on Fe content in these alloys. Then, the observations of peculiar clockwise hysteresis loops, wide double-step transitions and large magnetization fluctuations in glasses containing a large amount of Fe are analyzed to reveal a change in short range order with Fe content.