This study evaluates the input efficiency of greenhouse tomato and pepper farms in Kosovo. Using data collected from farm surveys, we conduct an input-oriented data envelopment analysis (DEA) to empirically assess input efficiency. Secondly, linear regression analysis is used to investigate which farm variables predict greenhouse tomato and pepper technical efficiency (TE). The DEA results indicated that among the seven regions in Kosovo, Prizren emerged as the most efficient greenhouse tomato producing region with a mean efficiency of 0.83 (on a scale of 0 to 1). Prishtina followed with a mean efficiency of 0.80. In the production of greenhouse peppers, Prishtina was the most efficient region with a mean efficiency of 0.99. Ferizaj followed with a mean efficiency of 0.93. Conclusions about farm characteristics that explain differences in efficiency were sensitive to model specification. Nevertheless, depending on the structural and operational characteristics of the greenhouse tomato and pepper farms, there is an opportunity for the technically inefficient farms and regions to improve their use of inputs.