Bacterial infections are a major complication in chronic obstructive pulmonary disease (COPD) and acute respiratory distress syndrome (ARDS), where mucus accumulation and pH fluctuations further hinder treatment. Nanostructured systems such as carbon dots (CDs) are increasingly investigated as antimicrobial agents due to their scalability, low cost, and biocompatibility, compared to conventional antibiotics. Here, CDs were synthesized by a one-step microwave-assisted method at three reaction temperatures (130 °C, 170 °C, and 185 °C, named LT-CDs, MT-CDs, HT-CDs, respectively) to explore the effect of carbonization on their structure and function. TEM, Raman, and FTIR analyses were employed to investigate the size and distribution of carbon groups. UV–vis confirmed distinct pH-dependent spectral responses, and mucoadhesion studies revealed stronger and more stable interactions for MT-CDs. Biological assays demonstrated high biocompatibility across all samples on lung fibroblasts, while antimicrobial tests highlighted a selective effect against Staphylococcus aureus, due to ROS generation. Overall, MT-CDs represented the best compromise in terms of size, functionalization, biocompatibility, mucoadhesion, and antimicrobial activity, emerging as promising nanoplatforms for respiratory infection management in COPD and ARDS.