The interferometric acquisition of the transmission matrix (TM) of a multimode optical fibre (MMF), which is at the heart of multimode fibre-based endoscopic imaging methods, requires using a reference beam. Attempts to use an internal reference, that is to provide the reference in a common pathway geometry through the MMF itself, lead to a speckled reference intensity and consequential occurrence of “blind spots”—locations where insufficient optical power in the reference wave inflicts strong measurement errors. Here we show that combining a relatively small number of TMs, which are measured using different internal references, facilitates a complete elimination of blind spots, and thereby a significant enhancement of the imaging quality.