Accelerometers collect data in an objective way, however, a number of decisions must be done during data collection, processing and output-interpretation. The influence of those decisions is seldom investigated, reported, or discussed. Herein, we examined the influence of different decisions on the outcomes: daily minutes of moderate-to-vigorous physical activity (MVPA), inactivity and light physical activity (LPA). In total, 156 participants wore an accelerometer (ActiGraph wGT3X-BT) on their nondominant wrist for 7 days. Data collection was conducted from February 2017 to June 2018. Data was processed using the R-package GGIR and default settings were compared to by-the-literature-suggested options. The output was examined using paired t-tests. When comparing two commonly used MVPA-cut-points, default and Hildebrand et al. we found a marginal difference (0.4 min, 1.0%, p < 0.001) in MVPA/day. When no bout criteria for MVPA/day was applied, MVPA/day was twice as high as bouted MVPA/day. Further, when we changed the epoch-length from 5to 1 s, statistically significant changes were seen for MVPA/day (-6.6 min, 19%, p < 0.001), inactivity/day (-22 min, 3.0%, p < 0.001) and LPA/day (28 min, 81%, p < 0.001). Decisions made during data processing of wrist-worn accelerometers has an influence on the output and thus, may influence the conclusions drawn. However, there may be situations when these settings are changed. If so, we recommend examining if the variables of interest are affected. We encourage researchers to report decisions made during data collection, processing and output-interpretation, to facilitate comparisons between different studies.