The coexistence of different properties in the same material often results in exciting physical effects. At low temperatures, the pyrite transition-metal disulphide NiS2 hosts both antiferromagnetic and weak ferromagnetic orders, along with surface metallicity dominating its electronic transport. The interplay between such a complex magnetic structure and surface-dominated conduction in NiS2, however, is still not understood. A possible reason for this limited understanding is that NiS2 has been available primarily in bulk single-crystal form, which makes it difficult to perform studies combining magnetometry and transport measurements with high spatial resolution. Here, NiS2 nanoflakes are produced via mechanical cleaving and exfoliation of NiS2 single crystals and their properties are studied on a local (micron-size) scale. Strongly field-asymmetric magnetotransport features are found at low temperatures, which resemble those of more complex magnetic thin film heterostructures. Using nitrogen vacancy magnetometry, these magnetotransport features are related to exchange-bias-type effects between ferromagnetic and antiferromagnetic regions forming near step edges at the nanoflake surface. Nanoflakes with bigger steps exhibit giant magnetoresistance, which suggests a strong influence of magnetic spin textures at the NiS2 surface on its electronic transport. These findings pave the way for the application of NiS2 nanoflakes in van der Waals heterostructures for low-temperature spintronics and superconducting spintronics.