An empirical methodology was developed for evaluating the fluid to particle heat transfer coefficient (hfp) and overall heat transfer coefficient (U) in bi-axially rotating cans. Conventional particle temperature measurement during thermal processing is generally difficult in cans undergoing agitation processing and is even more difficult in cans going through bi-axial free rotation as in continuous flow turbo cookers. Thin wire flexible thermocouples have helped in gathering temperature data of both particle and liquid in end-over-end batch processes. Wireless temperature loggers have been developed for liquid temperature measurements in continuous flow systems which can be used to estimate U. Evaluation of hfp is still difficult in these systems due to difficulty in gathering particle temperatures. The proposed method involves developing correlations between hfp and U using real time-temperature data gathered from test cans in fixed axial mode and then coupling them with experimentally evaluated U from fluid temperature gathered with wireless sensors to compute hfp for bi-axially rotating cans. The methodology is based on the assumption that within a can, factors that influence U will also influence hfp, and therefore hfp and U are generally interrelated. A three factor, five level central composite rotatatable design and a response surface methodology was used to develop the correlation models for the U and hfp in fixed axial mode with retort temperature (111.6–128.4 °C), glycerin concentration (80–100%), and rotational speed (4–24 rpm) as the main factors. The developed model was used to evaluate the U and hfp in the free bi-axial mode, using a full factorial design (3 × 3 factorial). The method was successfully implemented and an analysis of variance study, as expected, indicated all three major factors to influence the U and hfp values. Glycerin concentration and rotation speed were highly significant (<0.001), while temperature was marginally significant (p < 0.05) with respect to U while all factors were significant with hfp.