High-speed running (HSR) loads have been linked with non-contact injury risks in team-sports. This study investigated whether player-specific speed zones, reflecting individual fitness characteristics, impact the associations between non-contact injury and acute and chronic HSR loads. Semi-professional soccer players from two clubs (n = 47) were tracked over two seasons using 10 Hz GPS (5552 observations). HSR distances were calculated arbitrarily (≥5.5 m·s−1), and in an individualised fashion based on the final speed of the 30–15 intermittent fitness test. Cumulative running loads were represented by exponentially weighted moving averages with 7-(acute) and 28-day (chronic) decay parameters. Physiotherapists collected non-contact, lower-limb, time-loss injury data (n = 101). Injury models using session type (training vs matches), coach, as well as arbitrary or individualised running loads were constructed via mixed-effect logistic regression. Session type had the largest effect on injury (training vs match OR = 0.28; 95%CI:0.17–0.44). Variations in individualised or arbitrary acute and chronic HSR loads within the mid-range of the observed data had negligible effects on predicted injury risk. However, the uncertainty of estimated effects at extreme values of acute and chronic HSR loads prevented any conclusive findings. Therefore, the efficacy of using customised speed thresholds in quantifying load for injury risk mitigation purposes remains unclear.