Progress in layered van der Waals materials has resulted in the discovery of ferromagnetic and ferroelectric materials down to the monolayer limit. Recently, evidence of the first purely two-dimensional multiferroic material was reported in monolayer NiI2. However, probing multiferroicity with scattering-based and optical bulk techniques is challenging on 2D materials, and experiments on the atomic scale are needed to fully characterize the multiferroic order at the monolayer limit. Here, we use scanning tunneling microscopy (STM) supported by density functional theory (DFT) calculations to probe and characterize the multiferroic order in monolayer NiI2. We demonstrate that the type-II multiferroic order displayed by NiI2, arising from the combination of a magnetic spin spiral order and a strong spin-orbit coupling, allows probing the multiferroic order in the STM experiments. Moreover, we directly probe the magnetoelectric coupling of NiI2 by external electric field manipulation of the multiferroic domains. Our findings establish a novel point of view to analyze magnetoelectric effects at the microscopic level, paving the way towards engineering new multiferroic orders in van der Waals materials and their heterostructures.