This study examined the organizational factors affecting employee performance in non-governmental organizations (NGOs) in Uganda, with the Uganda Women Parliamentary Association (UWOPA) as a case study. The study was prompted by concerns about declining programme delivery efficiency, high staff turnover, and inconsistent project outcomes reported at UWOPA over the period 2019–2023. Three organisational factors—leadership style, organisational culture, and reward and compensation systems—were investigated as independent variables, while employee performance (assessed through task completion rates, work quality, and goal achievement) constituted the dependent variable. A cross-sectional design with mixed methods was employed. Data were collected from 86 UWOPA staff, including program officers, administrative staff, and management, using structured questionnaires supplemented by key informant interviews. Reliability coefficients (Cronbach's Alpha) ranged from 0.78 to 0.86. Descriptive statistics indicated moderate to high ratings across all organizational factors (means 3.38–3.74). Pearson's correlation revealed significant positive relationships between all three organizational factors and employee performance (r = 0.563 to 0.714, p < 0.01). Multiple regression analysis demonstrated that the three factors collectively explained 63.8% of the variance in employee performance (R² = 0.638, F = 32.47, p < 0.001). Leadership style emerged as the strongest predictor (β = 0.421, p < 0.001). The study concluded that leadership style is the most critical organizational determinant of employee performance at UWOPA, followed by organisational culture and reward systems. Recommendations include adoption of participatory leadership, organisational culture realignment, and enhanced performance-linked compensation.