<i>Background:</i> The use of respiratory therapist-directed (RD) protocols in non-ICU hospitalized patients decreases respiratory care charges as compared with physician-directed (PD) protocols. <i>Objectives:</i> To determine whether RD or PD protocol assessments in COPD patients may impact: (1) prescription of respiratory treatments, and (2) outcomes of pulmonary rehabilitation program (PRP). <i>Methods:</i> In a retrospective observational case-control study, 73 cases (RD) were compared with controls (PD) matched for age, sex, FEV₁ and diagnosis of either chronic airflow obstruction (CAO), pulmonary emphysema (PE) or chronic respiratory insufficiency (CRI). PRP programs were specifically tailored and assessed for inpatients with moderate to severe COPD. Type of PRP protocol (P), number of respiratory treatments (RT), number of exercise training prescription (EXP) and failure (EXF), time to start PRP (T) and length of hospital stay (LOS) were recorded. Perceived breathlessness (B) as assessed by MRC scale, 6-min walk meters (6MWD), and BORG-dyspnea at rest (D-rest) and end of effort (D-effort) were also assessed as outcome measures before (T0) and after (T1) the PRP. <i>Results:</i> Frequency distribution of P, EXP and EXF was similar in the two groups. However, prescription of additional RT (1.9 ± 0.8 and 2.5 ± 1.1 days, p < 0.01), T (1.2 ± 0.4 and 1.8 ± 1.2 days, p < 0.001) and LOS (17.2 ± 2.0 and 18.2 ± 1.8 days, p < 0.05) were lower in cases than in controls. Both cases and controls similarly improved (p < 0.0001) B, 6MWD, D-rest and D-effort at T1. <i>Conclusions:</i> RT-directed assessment results in less respiratory treatments prescription than PD-directed protocol and it does not affect the outcomes of in-hospital pulmonary rehabilitation of COPD patients.