In the present work, the liquid‐solid interaction of liquid N‐heteroaromatic compounds, commonly present in the petroleum feedstocks of the refineries, with Y zeolites used as hydrocracking catalysts was followed using IR‐ATR spectroscopy. The inhibition of the zeolitic acid sites by strongly basic pyridine and weakly basic indole was highlighted using a continuous flow IR‐ATR cell. Results were assessed by Density Functional Theory calculations to compute the vibrational frequencies of pyridine and indole according to the nature of the interaction sites: silanol groups or acidic OH groups. The study points out that IR‐ATR spectroscopy opens the way for investigating the interaction modes of low vapor pressure molecules (e. g. indole) that present an inherent difficulty to be operated in the gas phase. Moreover, the IR‐ATR makes possible the analysis of the little‐explored low wavenumber zone (<800 cm−1), that presents informative vibrational modes on the adsorption mode of N‐molecules. Hence, this work points out that for pyridine, the bands at 686 and 727 cm−1 are characteristic of pyridinium species formed over zeolitic OH groups, meanwhile, the signals at 703 and 750 cm−1, are associated to pyridine in interaction with silanol groups. The IR‐ATR study reveals that indole, a weakly basic compound, can be protonated on acidic Y zeolites as unambiguously evidenced by the formation of the bands at 1617, 1608, 1543 and 705 cm−1. Findings here exposed are crucial for studying inhibitory effects exerted by weak nitrogenated compounds on acidic materials during hydrocracking processes.