The study evaluated the effects of 12 weeks of multidisciplinary rehabilitation on functional recovery in 477 patients in Ecuadorian health centers, of which 354 (74.2%) had post-COVID-19 status (PCC) and 123 (25.8%) did not. Patients with PCC were younger at baseline (p=0.030), had more comorbidities (p<0.001), and differed by education, occupation, and type of provider. At 12 weeks, the PCFS score decreased by 0.48 points (95% CI −0.65 to −0.31, p<0.0001) and the AVS score increased by 0.68 points (95% CI 0.56–0.80, p<0.0001). In adjusted models, PCC at baseline was associated with lower odds of improvement in PCFS (aOR 0.27, 95% CI 0.13–0.56, p<0.001), while improvement in AVS did not differ (p=0.062). Follow-up completion was 73.6% at week 4, 69.2% at week 8, and 52.4% at week 12. The conclusion emphasizes improvement in functional status and perceived health, but less recovery in patients with PCC, which requires early identification and targeted rehabilitation.