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Sleep variability has been linked to poor subjective sleep quality, but few studies have investigated effects on physical health. In this study, we evaluated cross sectional associations and change over time in objective sleep variability of adults with insomnia and short sleep duration who were participating in a non-pharmacologic intervention study. Results indicated greater variability in objective sleep measures were associated with poorer subjective sleep quality (p < 0.05). Higher sleep duration variability was associated with higher HbA1c (p < 0.01) and sleep onset time variability was associated with higher BMI (p < 0.05). Sleep efficiency and WASO variability decreased with intervention (p < 0.05). These results indicate that objective sleep variability may be an important feature for the assessment of insomnia outcomes.