Trichoderma virens is a plant beneficial fungus that interacts intimately with roots and boosts plant immunity against invading pathogens. Some Trichoderma species have been used to control vascular wilt pathogen Fusarium oxysporum f. sp. cubense by enhancing host plant defence. In order to understand the molecular mechanisms of such interactions of Trichoderma with banana roots, this study analyses the secretome of T. virens induced by tissue culture raised banana cv. Rasthali roots, using a gel-free proteome approach. Tissue cultured banana roots were co-incubated with germinated conidia of T. virens for four days. The filtrate was harvested and proteins were identified using mass spectrometry (trypsin digestion and LC-MS/MS analysis). A total of 77 proteins were identified to be upregulated in T. virens in contact with banana roots, compared with T. virens incubated alone. Among these, 11 and 6 belonged to the glycoside hydrolases and small cysteine-rich secreted proteins (SSCPs), respectively. These two groups of proteins are known to be involved in plant-Trichoderma interactions, facilitating penetration, colonization, and inducing defense responses. Contrary to this, 27 proteins were downregulated in contact with banana roots and 32 did not show any significant changes. This is the first study on proteome analysis of Trichoderma in contact with banana roots leading to the identification of potential elicitor proteins that could be relevant to disease management in banana. A novel cerato-platanin family protein and a Nep-1 like protein were found to be upregulated in contact with banana roots. Since such proteins are known to be involved in plant-microbe interactions, these are being studied for their role in Trichoderma-banana plant interactions especially in induced defence.