Molecules intercalating two-dimensional materials form complex structures that have been characterized primarily by spatially averaged techniques. Here we use aberration-corrected scanning transmission electron microscopy and density-functional-theory (DFT) calculations to study the atomic structure of bilayer graphene (BLG) and few-layer graphene (FLG) intercalated with FeCl3. In BLG, we discover two distinct intercalated structures that we identify as monolayer FeCl3 and monolayer FeCl2. The two structures are separated by atomically sharp boundaries and induce large free-carrier densities on the order of 1013cm−2 in the graphene layers. In FLG, we observe multiple FeCl3 layers stacked in a variety of possible configurations with respect to one another. Finally, we find that the microscope's electron beam can convert the FeCl3 monolayer into FeOCl monolayers in a rectangular lattice. These results reveal the need for a combination of atomically resolved microscopy, spectroscopy, and DFT calculations to identify intercalated structures and study their properties.