This report is the first research study that aims to explore the molecular mechanisms involved in the in vitro pulmonary cytotoxicity triggered by long-term exposure to silicon-based quantum dots (QDs). Human lung fibroblasts (MRC-5 cell line) were exposed to 5 µg/mL silicon-based QDs for 5 weeks and the concentration was increased up to 40 µg/mL QDs during the next 4 weeks. Cell viability and population doubling level were calculated based on Trypan blue staining. The expression levels of proteins were established by Western blotting and the telomeres’ length was determined through Southern blotting. Prolonged exposure of lung fibroblasts to QDs reduced the cell viability by 10% compared to untreated cells. The level of p53 and apoptosis-inducing factor (AIF) expression increased during the exposure, the peak intensity being registered after the seventh week. The expressions of autophagy-related proteins, Beclin-1 and LC-3, were higher compared to untreated cells. Regarding the protein expression of Nrf-2, a progressive decrease was noticed, suggesting the downregulation of a cytoprotective response to oxidative stress. In contrast, the heat shock proteins’ (HSPs) expression was increased or maintained near the control level during QDs exposure in order to promote cell survival. Furthermore, the telomeres’ length was not reduced during this exposure, indicating that QDs did not induce cellular senescence. In conclusion, our study shows that silicon-based QDs triggered the activation of apoptotic and autophagy pathways and downregulation of survival signaling molecules as an adaptive response to cellular stress which was not associated with telomeres shortening.