The influence of the smokestack emissions of a ground-level train in the air quality of the passenger carriages through the ventilation system was investigated in this work. To this end, a monitoring campaign was designed and implemented at 20 different in-train sites, e.g., conductor’s cabin, carriages with passenger seats, boarding carriages, spaces for disabled people, etc., during its journey between urban and rural areas. Measurements of inorganic (NOx, SO2, CO) and organic (benzene, polyaromatic hydrocarbons, total volatile organic compounds) compounds as well as airborne particulate matter (PM) in different size ranges (ΡΜ10, ΡΜ2.5, ΡΜ1) were carried out in the interior of the carriages of a diesel engine-powered train (type KAT 2000) during fixed round trips. An exhaust dispersion cone hook was used for intervention purposes leading to the reassessment of the in-train air quality at the most contaminated sites. In order to produce reliable and comparable data, targeted measurements were conducted in a railbus which was used as reference. Based on the analysis, the air pollutants and particle levels exhibit significant variations at the same sampling point during the train journey, possibly due to the route characteristics (tunnels, uphills, turns, speed). Significant spatial fluctuations in the same train depending on the position and the proximity to the smokestack plume and the ventilation system inlet were observed as well. It is worthy to note that decreased pollutant values were observed during the intervention.