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In the device-independent quantum information approach, the implementation of a given task can be self-tested solely from the recorded statistics and without detailed models for the employed devices. Even though experimentally demanding, it provides appealing verification schemes for advanced quantum technologies that naturally fulfil the associated requirements. In this work, we experimentally study whether self-testing protocols can be adopted to certify the proper functioning of new quantum devices built with modern space-division multiplexing optical fiber technology. Specifically, we consider the prepare-and-measure protocol of M.~Farkas and J.~Kaniewski (Phys.~Rev.~A 99, 032316) for self-testing measurements corresponding to mutually unbiased bases (MUBs) in a dimension $d>2$. In our scheme, the state preparation and measurement stages are implemented with a multi-arm interferometer built with new multi-core optical fibers and related components. Due to the high-overlap of the interferometer's optical modes achieved with this technology, we are able to reach the required visibilities for self-testing the implementation of two four-dimensional MUBs. We also quantify two operational quantities of the measurements: (i) the incompatibility robustness, connected to Bell violations, and (ii) the randomness extractable from the outcomes. Since MUBs lie at the core of several quantum information protocols, our results are of practical interest for future quantum works relying on space-division multiplexing optical fibers.