The present paper is concerned with the development of a custom pulsed ultrasound velocity profiling (PUV) methodology to non-invasively measure, analyze and control protein melt flow and power-law flow indices in the cooling die during high moisture (HME) extrusion processing. The methodology is first validated on glycerol and a carboxymethyl cellulose (CMC) solution as Newtonian and shear-thinning reference fluids, respectively, at different flow rates followed by application to two pea protein melts at different moisture contents (MCs) in the low flow rate regime typical of a pilot-scale extruder and characterized by a poor signal to noise ratio (SNR) close to the extruder die wall. The flow indices were compared with those obtained from conventional rheometry, showing good agreement for the reference fluids and semi-quantitative agreement for the protein melts. The study confirms that PUV can be used for in-line application in a cooling die by measuring the local flow conditions, as well as contribute to the understanding of protein melt fibre formation. On the other hand, the SNR close to the die wall need to be improved e.g. by using an ultrasound transducer operating at higher frequency and modifying the die to enable quantitative agreement with flow simulations to properly extract local rheometric data. Thus, it is concluded that further refinement of the methodology is both possible and needed to improve the accuracy of the measurements in future work for in-line application during HME extrusion.