The increasing adoption of flexible work practices and Agile methodologies in modern organizations has highlighted the need for a deeper understanding of the factors that influence employees’ Work–Life Integration. Therefore, this study aims to examine the effects of Agile Scrum and Workplace Flexibility on Work–Life Integration among startup employees in Depok City, Indonesia, while investigating the mediating role of Perceived Autonomy. Primary data were collected through a questionnaire survey involving 20 respondents and analyzed using the Structural Equation Modeling–Partial Least Squares (SEM-PLS) approach with SmartPLS software. Statistical significance was assessed through a non-parametric bootstrapping procedure. The results revealed that Agile Scrum had a positive and significant effect on Work–Life Integration (β = 0.462, p = 0.003), whereas Workplace Flexibility had a positive and significant effect on Perceived Autonomy (β = 0.675, p < 0.001). In contrast, Agile Scrum did not have a significant effect on Perceived Autonomy, Workplace Flexibility did not significantly affect Work–Life Integration, and Perceived Autonomy did not significantly influence Work–Life Integration. These findings suggest that Agile Scrum contributes directly to enhancing employees’ Work–Life Integration, while Workplace Flexibility primarily strengthens employees’ perceptions of autonomy rather than directly improving the integration of work and personal life. The study provides empirical insights into the mechanisms through which Agile work practices and flexible work environments influence employee well-being in startup organizations.
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