The vegetable sector holds significant importance for farmers' income in Nepal, yet the unsystematic use of chemical fertilizers and pesticides is challenging the sustainability of the sector. This signifies the need to adopt Good Agriculture Practices (GAP) to ensure food safety and minimize negative environmental impacts. Understanding the influencing factors, both positive and negative, is essential when transitioning to GAP-based production. To bridge this knowledge gap, a study was conducted in the Kathmandu Valley, employing a mixed-method approach including farmers’ surveys, key informant interviews, and in-depth interviews. The stepwise linear regression analysis revealed that tomato production and labor cost demonstrated a positive and significant (p < 0.001) relationship with the area under GAP-based vegetable production. Additionally, positive correlations were observed (p < 0.05) between the amounts of improved compost application, and vermicompost application with the area under GAP-based vegetable production. However, a negative and significant (p < 0.001) relationship was observed between the amount of botanical application and the area under GAP-based vegetable production. Given that food safety and sustainability are global concerns, the findings of this study could provide practical guidance for policymakers, agricultural practitioners, and farmers to develop targeted interventions and policies that promote GAP widely.