The ongoing trend toward miniaturization has led to an increased interest in the magnetoelectric effect, which could yield entirely new device concepts, such as electric field-controlled magnetic data storage. As a result, much work is being devoted to developing new robust room temperature (RT) multiferroic materials that combine ferromagnetism and ferroelectricity. However, the development of new multiferroic devices has proved unexpectedly challenging. Thus, a better understanding of the properties of multiferroic thin films and the relation with their microstructure is required to help drive multiferroic devices toward technological application. This review covers in a concise manner advanced analytical imaging methods based on (scanning) transmission electron microscopy which can potentially be used to characterize complex multiferroic materials. It consists of a first broad introduction to the topic followed by a section describing the so-called phase-contrast methods, which can be used to map the polar and magnetic order in magnetoelectric multiferroics at different spatial length scales down to atomic resolution. Section 3 is devoted to electron nanodiffraction methods. These methods allow measuring local strains, identifying crystal defects and determining crystal structures, and thus offer important possibilities for the detailed structural characterization of multiferroics in the ultrathin regime or inserted in multilayers or superlattice architectures. Thereafter, in Section 4, methods are discussed which allow for analyzing local strain, whereas in Section 5 methods are addressed which allow for measuring local polarization effects on a length scale of individual unit cells. Here, it is shown that the ferroelectric polarization can be indirectly determined from the atomic displacements measured in atomic resolution images. Finally, a brief outlook is given on newly established methods to probe the behavior of ferroelectric and magnetic domains and nanostructures during in situ heating/electrical biasing experiments. These in situ methods are just about at the launch of becoming increasingly popular, particularly in the field of magnetoelectric multiferroics, and shall contribute significantly to understanding the relationship between the domain dynamics of multiferroics and the specific microstructure of the films providing important guidance to design new devices and to predict and mitigate failures.