Recent resting-state functional connectivity fMRI (RS-fcMRI) research has demonstrated that head motion during fMRI acquisition systematically influences connectivity estimates despite bandpass filtering and nuisance regression, which are intended to reduce such nuisance variability. We provide evidence that the effects of head motion and other nuisance signals are poorly controlled when the fMRI time series are bandpass-filtered but the regressors are unfiltered, resulting in the inadvertent reintroduction of nuisance-related variation into frequencies previously suppressed by the bandpass filter, as well as suboptimal correction for noise signals in the frequencies of interest. This is important because many RS-fcMRI studies, including some focusing on motion-related artifacts, have applied this approach. In two cohorts of individuals (n=117 and 22) who completed resting-state fMRI scans, we found that the bandpass–regress approach consistently overestimated functional connectivity across the brain, typically on the order of r=.10–.35, relative to a simultaneous bandpass filtering and nuisance regression approach. Inflated correlations under the bandpass–regress approach were associated with head motion and cardiac artifacts. Furthermore, distance-related differences in the association of head motion and connectivity estimates were much weaker for the simultaneous filtering approach. We recommend that future RS-fcMRI studies ensure that the frequencies of nuisance regressors and fMRI data match prior to nuisance regression, and we advocate a simultaneous bandpass filtering and nuisance regression strategy that better controls nuisance-related variability. •Bandpass filtering and nuisance regression are intended to reduce noise in RS-fMRI.•When RS-fMRI data are filtered, but regressors are not, noise is poorly controlled.•In addition, this approach reintroduces synchronous noise into RS-fMRI data.•Such noise leads to systematically inflated estimates of functional connectivity.•Simultaneous bandpass filtering and regression eliminates this source of bias.