Duathlon consists of two durations of running separated by cycling in a format similar to triathlon. The addition of cycling and the associated loadings on the neuromuscular system can modify spatiotemporal variables in running including trunk motion, which can impact running economy. Changes to trunk motion can be inferred by measuring accelerations of the centre of mass (CoM). However, there is scarce research into trunk dynamics in duathlon. Therefore, the aim of this study was to use an inertial sensor (an accelerometer) to compare acceleration magnitudes of the trunk in the vertical, mediolateral, and anteroposterior directions during a simulated field-based duathlon. Specifically, running performance and magnitudes of trunk acceleration were compared pre and post a cycling load. Ten well-trained duathletes (seven males, three females (mean ± SD; age: 31.1 ± 3.4 years; body mass: 70.9 ± 6.9 kg; body height: 177 ± 5.82 cm; 9.45 ± 1.7 weekly training hours per week; 9.15 ± 5.2 years training experience)) completed a 5 km run performed at a self-selected pace (described as moderate intensity) prior to 20 km of continuous cycling at four varied cadence conditions. This was immediately followed by a 2.5 km run. Mean completion times for the final 2.5 km in running pre-cycling (4.03:05 ± 0.018) compared to the 2.5 km in running post-cycling (4.08:16 ± 0.024) were significantly different. Regarding trunk acceleration, the largest difference was seen in the vertical direction (y axis) as greater magnitudes of acceleration occurred during the initial 1 km of running post-cycling combined with overall significant alterations in acceleration between running pre- and post-cycling (p = 0.0093). The influence of prior cycling on trunk acceleration activity in running likely indicates that greater vertical and mediolateral trunk motion contributes to decremental running performance. In future, further advanced simulation and analysis could be performed in ecologically valid contexts whereby multiple accelerometers might be used to model a more complete set of dynamics.