Aims. We analyse synthetic emission maps of the [CII] 158 mu m line and far-infrared (FIR) continuum of simulated molecular clouds (MCs) within the SILCC-Zoom project to study the origin of the observed [CII] deficit, that is, the drop in the [CII]/FIR intensity ratio caused by stellar activity. Methods. All simulations include stellar radiative feedback and the on-the-fly chemical evolution of hydrogen species, CO, and C+. We also account for further ionisation of C+ into C2+ inside HII regions, which is crucial to obtain reliable results. Results. Studying individual HII regions, we show that I-FIR is initially high in the vicinity of newly born stars, and then moderately decreases over time as the gas is compressed into dense and cool shells. In contrast, there is a large drop in I-CII over time, to which the second ionisation of C+ into C2+ contributes significantly. This leads to a large drop in I-[CII] /I-FIR inside HII regions, with I-[CII] /I-FIR decreasing from 10(-3)-10(-2) at scales above 10 pc to around 10(-6)-10(-4) at scales below 2 pc. However, projection effects can significantly affect the radial profile of I-[CII]/I-FIR, and their ratio, and can create apparent HII regions without any stars. Considering the evolution on MC scales, we show that the luminosity ratio, L-[CII]/L-FIR, decreases from values of greater than or similar to 10(-2) in MCs without star formation to values of around similar to 10(-3) in MCs with star formation. We attribute this decrease and thus the origin of the [CII] deficit to two main contributors: (i) the saturation of the [CII] line and (ii) the conversion of C+ into C2+ by stellar radiation. The drop in the L-[CII]/L-FIR ratio can be divided into two phases: (i) During the early evolution of HII regions, the saturation of [CII] and the further ionisation of C+ limit the increase in L-[CII], while L-FIR increases rapidly, leading to the initial decline of L-[CII]/L-FIR. (ii) In more evolved HII regions, L-CII stagnates and even partially drops over time due to the aforementioned reasons. L-FIR also stagnates as the gas gets pushed into the cooler shells surrounding the HII region. In combination, this keeps the global L-[CII]/L-FIR ratio at low values of similar to 10(-3).