Improving agricultural productivity has received considerable policy intervention in many African countries and particularly in Rwanda. The question remains to know the extent to which the policy contributes to the variation being upwards or downwards of the crop productivity. There are number of determinant factors some being personal and others institutional. This study examines the variation of agricultural productivity to document the extent to which agricultural productivity has shifted and what factors have contributed to the shift, with focus to the voucher system and the land use consolidation introduced by the Ministry of Agriculture in Rwanda. Secondary data were collected to describe the trends in agricultural productivity in Nyamagabe District, Southern Province in Rwanda. In addition, a household survey of 100 households was conducted in two Cells of Kamegeri Sector to assess at household level how the agricultural policy has contributed to the shifting of agricultural productivity. This shift is time-bounded and effects of agricultural policy are gradual overtime. Results from the analysis of secondary data show that greater agricultural productivity for both food and cash crops grown in Nyamagabe District is observed mostly in the period starting from 2007 and onwards. This period coincides with more policy innovations and interventions including the Crop Intensification Programme and specifically the introduction of the voucher system, land use consolidation and crop regionalization. To validate these macro-level findings, the Probit and Instrumental variable models were estimated to establish the marginal effects of these policy interventions on agricultural productivity measured by yield at household level. Findings substantiate that the voucher system has significant marginal effects on change in crop yield (measured by farmer’s perception) at 5% level of significance (Z= 2.41 P> [Z] =0.016 and Z= 2.77, P> [Z] =0.006). Further policy innovations and interventions should focus on how farmers can maintain the same momentum themselves beyond policy interventions in Rwanda.