Intermodal freight transport is an integral, strategic foundation of the European Union’s vision to decarbonize Europe, but in non-EU countries such as Republic of Serbia, the split in modalities remains heavily focused on road haul, while terminal infrastructure remains poorly interconnected and digital maturity remains low. This research study investigates the adoption of new digital and operational technologies along the intermodal transport chain. It is measured in the context of enhancing ecological and operational performance in the Serbian environment. Research data was collected from a sample of nine medium and large Serbian intermodal logistics companies, who operate along Pan-European Corridor X and the Rhine–Danube Corridor. Three ecological and three operational key performance indicators (KPIs) were defined to measure the level on enhancements reached through sustainability efforts. The study is an uncontrolled, firm-level pre–post comparison: three directional hypotheses were evaluated using paired-sample t-tests, exact Wilcoxon signed-rank tests, and bootstrap confidence intervals on pre- and post-modernization firm-level aggregates. In the post-modernization period, mean CO₂ intensity per TEU (twenty-foot equivalent unit) was 17.4% lower, terminal energy intensity (kWh/TEU) 14.3% lower, and terminal dwell time 22.5% lower than in the pre-modernization period (exact p ≤ 0.001; 95% bootstrap confidence intervals excluding zero). Implications were discussed for EU Green Deal alignment, Trans-European Transport Network (TEN-T) extension to the Western Balkans, and future research has been initially defined. Given the pre/post design without a control group, the reported effects are associations rather than causal estimates and should be read as preliminary, exploratory evidence.