Single-use solid oral dosage forms have to be compounded for pediatric patients due to a lack of pediatric-licensed formulations or for small scale studies. Low content uniformity of such dosage forms, especially capsules, is a cause of variation of e.g. steroid doses in children. Besides quantification, identification of active pharmaceutical ingredients in different hard-shell capsules using different excipients can play a role, especially when ensuring the blinding effectiveness of investigational medical products or when rapid unblinding in case of emergency is necessary. Non-destructive quality control of compounded closed hard shell capsules containing very low doses is therefore highly rewarding. The individual control of a whole batch of pediatric capsules intended to be administered is possible, due to near-infrared spectroscopy (NIRS) being a rapid and non-destructive technique. FT-NIR spectroscopy with investigational sample preparation and custom-designed, 3D-printed sample holders were used to examine the capsules. This method ensures the results to be reproducible. Different chemometric approaches, which use the Mahalanobis distance, were applied to the data. Partial least squares regression (PLSR) was used to achieve the quantification of the content of hydrocortisone acetate in the capsules. While the identification of captopril, hydrochlorothiazide, and sildenafil citrate mixed with various excipients in closed hard shell capsules could be achieved, non-destructive quantification of very low doses of main real-life example hydrocortisone acetate remains an issue.