This study aimed to analyse the effects of shoes with increased longitudinal bending stiffness (LBS) on 3,000 m performance, pacing strategy, heart rate, and biomechanics in trained runners. Twelve male trained runners performed a 3,000 m time trial test in an experimental shoe with a carbon fibre plate to increase the LBS (LBS-increased) and a Control shoe (without carbon fibre plate). Running performance (total time), pacing, heart rate, and biomechanical variables were registered and analysed for each 1000 m split. An individual analysis of the responders was performed based on the smallest worthwhile change. The 3,000 m time trial performance improved by 0.74% (585.83 ± 33.39 vs. 590.17 ± 34.35 s, p < 0.001, large d = 0.829) in the LBS-increased condition compared to the Control condition with a high inter-individual variability. There were no significant differences for the split effect (p = 0.898, small ηp2 = 0.021). The performance improvement was accompanied by an increase in step length (p < 0.001, large ηp2 = 0.717) throughout the time trial test and an increase of flight time in the split 1 and 2 (p < 0.05, moderate d = 0.793, 0.686, respectively) and vertical oscillation in the split 2 and 3 (p < 0.05, moderate d = 0.727, 0.652). However, the heart rate remained unchanged between conditions. The increase of LBS in footwear can improve 3,000 m performance without causing changes in the pacing strategy. Small modifications in running kinematics accompanied the improvements in running performance but without changes in heart rate. Moreover, LBS-increased did not affect all runners equally highlighting the need for further understanding of individual responses.