Agriculture uses land resources and also contributes to environmental degradation through intensification and over exploitation of resources. Biodiversity loss, particularly in the Netherlands, has become a concern. The loss has been addressed amongst other measures through agri-environment schemes (AES) but its effects still remain questionable. Several studies have presented contradicting results on the impacts of AES in the Dutch agriculture. Previous studies have concluded that management agreements have had no positive effects on plants and birds diversity. The effects of management agreements for botanic contract have been investigated on entire fields or field edges and results showed no positive effects. This research has sought to investigate effects of AES on agricultural inputs and outputs and why AES has not benefited biodiversity substantially in the Netherlands based on previous research. The methodology applied were interviews, use of questionnaire, inputs-outputs analysis and literature review. Experts and farmers within the Netherlands formed the respondents for this research. Researchers who have done similar study on AES were interviewed to solicit for their knowledge on the research topic. Also, experts who are leaders and advisors of farmer cooperative and working in nature conservation organizations were consulted. The selection criterion of farmers was based on those who have accepted AES contracts basically, for botanic scheme and meadow birds’ protection. Topics outlined in the questionnaire include effects of AES on inputs and outputs, effects of AES on biodiversity, effects of AES on production, effects on natural resources, economic impacts of AES, issues that hinder AES to benefit biodiversity substantially and suggestions for improvement. Results from interviews conducted show that short contract duration, low and irregular payments, inefficient monitoring, bureaucracy and agricultural intensification are issues that hinder agri-environment schemes to benefit biodiversity substantially. Extending contract durations, improving payments, reducing bureaucracy and making management prescriptions flexible are recommendations proposed to improve agri-environment schemes to enhance biodiversity.