(1) Background: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative condition, whose bulbar involvement compromises language, swallowing, and airway protection. When oral nutrition is no longer adequate, percutaneous endoscopic gastroscopy (PEG) may be indicated. However, as exact timing is still debatable, we tried to find it. (2) Methods: A prospective cohort study was performed using fiber-optic endoscopic evaluation of swallowing (FEES), functional evaluation scales (ALS Functional Rating Scale-Revised (ALSFRS-R) and bulbar sub-score (ALSFRS-R-B)), lung function tests (like Forced Vital Capacity (FVC), Cough Peak Flow (CPF)) and anthropometric data. (3) Results: Twenty-three patients were enrolled (mean 65.4 ± 9.1 years, 60.9% males), 12 with spinal-onset. During the study period, 58 FEES were performed (1–4/patients). Even before formal PEG indication, suggestions were given to correct the alterations found. PEG was placed in 12 patients, on average 21.8 months after diagnosis (FVC = 69.9% ± 26.7%, ALSFRS-R-B = 7.7 ± 3.7, ALSFRS-R = 28.9 ± 12.3), and being 91.7% under ventilatory support. ALSFRS-R-B, CPF, FVC, and ALSFRS-R showed significant discriminant ability for PEG placement. Sensitivity and specificity were, respectively, ALSFRS-R-B ≤ 8 (100/90.9), CPF ≤ 205 (83.3), FVC ≤ 74 (83.3/74.2), and ALSFRS-R < 29 (83.3/65.1). (4) Conclusions: FEES provide additional information beyond formal PEG indication. ALSFRS-R-B score ≤ 8 was found as a best functional and noninvasive indicator for PEG placement in ALS patients.