Multiwalled carbon nanotubes (MWCNTs) are attractive materials for realizing sensors, owing to their high aspect ratio associated with excellent mechanical, electronic, and thermal properties. Moreover, their sensing properties can be tuned by introducing functional groups on their framework and adjusting the processing conditions. In this paper, we investigate the potential of functionalized CNTs for humidity and temperature sensing by optimization of the functionalization, the processing conditions and the printing conditions. The morphology of the differently functionalized MWCNTs is investigated by infrared spectroscopy (IR), scanning electron microscopy, thermogravimetry (TG) and TG-coupled mass-spectrometric studies. Using the functionalized MWCNTs, films were fabricated with different numbers of layers (4, 6, 8, 10 layers) via inkjet printing on a flexible polyimide substrate containing an interdigital microelectrode. The influence of hydrothermal effects was investigated. The sensitivity to humidity is higher for films prepared with MWCNTs functionalized with a high sonication amplitude and a bigger number of layers due to enhancements of hydrophilicity and water mobility. A higher sensitivity to temperature is achieved by a low sonication amplitude and a small number of layers. For the encapsulation of the temperature sensor against humidity, a Bectron layer is proposed, which reduces also the hysteresis effect. This study demonstrates the efficiency of carboxylic functionalized MWCNTs deposit by inkjet printing for realization of sensitive and cost-effective humidity and temperature sensors. It provides a real example for the interesting contribution of functionalization procedures to the sensing properties of MWCNTs films.