The aim of this study was to determine possible influences, including data processing and sport-specific demands, on the validity of acceleration measures by an inertial measurement unit (IMU) in indoor environments. IMU outputs were compared to a three-dimensional (3D) motion analysis (MA) system and processed with two sensor fusion algorithms (Kalman filter, KF; Complementary filter, CF) at temporal resolutions of 100, 10, and 5 Hz. Athletes performed six team sport-specific movements whilst wearing a single IMU. Mean and peak acceleration magnitudes were analyzed. Over all trials (n = 1093), KF data overestimated MA resultant acceleration by 0.42 ± 0.31 m∙s−2 for mean and 4.18 ± 3.68 m∙s−2 for peak values, while CF processing showed errors of up to 0.57 ± 0.41 m∙s−2 and −2.31 ± 2.25 m∙s−2, respectively. Resampling to 5 Hz decreased the absolute error by about 14% for mean and 56% for peak values. Still, higher acceleration magnitudes led to a large increase in error. These results indicate that IMUs can be used for assessing accelerations in indoor team sports with acceptable means. Application of a CF and resampling to 5 Hz is recommended. High-acceleration magnitudes impair validity to a large degree and should be interpreted with caution.