Background: Incomplete data due to nonparticipation and noncompliance with the study protocol can bias the results of studies. We investigated how a nationwide accelerometer sample of adolescents and young adults is affected by such incomplete data. Methods: We analyzed cross-sectional data from 6465 participants (11–31 y old) who participated in a national health survey in Germany (KiGGS Wave 2; 2014–2017). The data included information about the participation in the measurement of physical activity using accelerometers, compliance with the wear-time protocol, and sociodemographic and health-related variables. Multivariable regression analyses were conducted to detect factors associated with incomplete data. Results: Of the total sample, 78.0% participated in the accelerometer part of the study, and 83.5% of the participants with data available complied with the wear-time protocol. In 11- to 17-year-olds, the likelihood of having incomplete accelerometer data was higher in boys, older adolescents, adolescents with a lower sociodemographic status, adolescents with overweight, adolescents not participating in organized sport, adolescents not speaking only German at home, current smokers, and adolescents having a higher soft drink consumption. In 18- to 31-year-olds, the likelihood of having incomplete accelerometer data was higher in men, adults with a lower educational level, adults not speaking only German at home, and adults who smoke. Conclusions: Our results suggest that accelerometer samples are biased such that participants with more beneficial health behaviors provide complete accelerometer data more often. This knowledge should be used to design effective recruitment strategies and should be considered when interpreting results of accelerometer studies.