The nanoscale structural properties of ultrathin (2 nm high) self-assembled (0 0 0 1) polar and (11-22) semipolar InGaN/GaN quantum dot (QD) superlattices, grown by plasma-assisted molecular beam epitaxy, were investigated using transmission electron microscopy (TEM) techniques. Samples grown under two sets of temperature ranges were compared. The higher-temperature uncapped polar QDs were well-defined and exhibited a truncated pyramidal morphology. Similar morphology was observed for the embedded QDs, albeit faintly diffused. On the other hand, the polar superlattices grown at lower temperatures were heavily distorted due to a large stacking fault density. Semipolar QDs exhibited lenticular morphology. The QD superlattices were found to be elastically strained using geometrical phase analysis, and their strain state was well-described by a biaxial approximation. The extrapolated indium content was consistent with reduced indium incorporation efficiency for the semipolar case compared with the polar one.