Background: Bronchiectasis exacerbations are often treated with prolonged antibiotic use, even though there is limited evidence for this approach. We therefore aimed to investigate the baseline clinical and microbiological findings associated with long courses of antibiotic treatment in exacerbated bronchiectasis patients. Methods: This was a bi-centric prospective observational study of bronchiectasis exacerbated adults. We compared groups receiving short (≤14 days) and long (15–21 days) courses of antibiotic treatment. Results: We enrolled 191 patients (mean age 72 (63, 79) years; 108 (56.5%) females), of whom 132 (69%) and 59 (31%) received short and long courses of antibiotics, respectively. Multivariable logistic regression of the baseline variables showed that long-term oxygen therapy (LTOT), moderate–severe exacerbations, and microbiological isolation of Pseudomonas aeruginosa were associated with long courses of antibiotic therapy. When we excluded patients with a diagnosis of community-acquired pneumonia (n = 49), in the model we found that an etiology of P. aeruginosa remained as factor associated with longer antibiotic treatment, with a moderate and a severe FACED score and the presence of arrhythmia as comorbidity at baseline. Conclusions: Decisions about the duration of antibiotic therapy should be guided by clinical and microbiological assessments of patients with infective exacerbations.