Considering the continuous development of ytterbium (Yb)-doped fibers for fiber lasers and amplifiers, thorough characterization of the features and quality of such fibers is necessary now more than ever. In particular, the evaluation of the very strong core attenuation that results from Yb absorption and the losses accompanying photodarkening (PD) processes in Yb-doped optical fibers is still of immense interest. Keeping that in mind, the potential of a method using pinhole fibers will be demonstrated here. Moreover, the investigation of fluorescence properties of Yb3+ is also important; it can be affected by phenomena such as reabsorption, inhomogeneous pump intensity distribution, amplified spontaneous emission, lasing, and, lastly, PD. As these phenomena occur while measuring the fluorescence properties of Yb3+ in optical fibers, they can distort the fluorescence spectra and fluorescence decay significantly. We suggest a twice-perpendicular measurement method and strict time management to avoid these interfering phenomena during the fluorescence measurements.