This study provides empirical evidence that CO₂ emissions from transport (total and by transport types) have an impact on countries’ logistics efficiency, both in general (Logistics Performance Index) and in terms of its individual indicators (volumes of freight transport (total and by transport types) and total investments in transport infrastructure). The aim is to empirically demonstrate the impact of CO₂ emissions from different modes of transport on the logistics efficiency of countries, specifically using data from 60 International Transport Forum (ITF) member countries. The Granger causality analysis, based on VAR modeling for six periods evaluated by the World Bank (2007, 2010, 2012, 2014, 2016, 2018), demonstrates that in 50% of the countries, changes in CO₂ emissions from transport are the cause of the shifts in the Logistics Performance Index (increasing emissions can impede logistics efficiency). The sample was reduced to these countries for the regression modeling. Regression modeling (with fixed and random effects, Hausman test, for 2002–2021 on panel data for countries in which direct causality was confirmed) showed that a one-unit increase in total CO2 emissions from transport (in general and in air transport) is associated with 0.12 and 0.21 decrease in total investments in transport infrastructure. An increase in road CO2 emissions is associated with a 0.49 decrease in road freight transport (ton-km per thousand units of GDP). An increase in CO2 rail emissions is associated with a 0.15 increase in total investments in transport infrastructure and a 0.12 increase in total freight transport.