In response to growing environmental concerns in the textile industry, this study investigates the effects of a low-pressure glow discharge (LPGD) plasma with oxygen (O2) and nitrogen (N2) gases on the dyeing process of jute-cotton (JC) blended fabrics, using coffee extract as a natural dye source. The hydrophilic properties of all the JC blended fabric samples were enhanced due to plasma treatments. The contact angles of the samples were significantly decreased from 131° to 52° (O2) and 55° (N2) after 20 minutes of plasma treatment. Compositional analysis revealed new functional groups e.g., CO and N−H, on the fabric's surface after plasma treatment. Surface morphology analysis indicated that the surface roughness of the treated fabric was increased with plasma treatment time. The improvement of the wicking properties of the fabric with contact time was also observed. All the plasma-treated fabric samples exhibited good colour strength (k/s), wash fastness, and rubbing fastness. After plasma treatment with O2 gas for 20 minutes, the k/s value had increased from 3.6 to 4.9. Washing and rubbing (dry) color fasting ratings were enhanced from 1 to 3 and 2–4, respectively, following a 20-minute plasma treatment with O2 gas. Although both O2 and N2 plasma treatment showed a significant impact on the dyeing properties of JC blended fabric, O2 gas provided better results compared to N2 gas plasma treatment.