The research discusses the evaluation of organization performance using Balance Scorecard approach (financial perspective, customer perspective, internal business perspective, growth and learningt perspective) that boosts long term performance success and measure thoroughly. The objective of the research was to compare the organization performance between Bank Madina Syariah and LAZISMU PDM in empowering ZIS fund with different managerial system using descriptive qualitative approach. LAZISMU PDM has good level of satisfaction toward the perspective of the customers or mustahik based on society empowerment (productive) since LAZISMU PDM uses family system as the form of supervision. Meanwhile, Bank Madina Syariah is the opposite of LAZISMU PDM since the bank’s management system does not have fund empowerment program in productive sector. Bank Madina Syariah has better score that LAZISMU PDM with the operational system that applies professional zakat since the operational system of LAZISMU PDM is complicated and there is no understanding with the services offices. The growth and learning perspective of LAZISMU PDM which is based on the training of the SDM (Human Resources) is not good yet compared to Bank Madina Syariah since the efforts to improve the staff’ performance are still dominated by the spirits to perform religious rituals and loyalty. Meanwhile, Bank Madina Syariah always provide trainings and set targets toward the staff. Lastly, LAZISMU PDM has better growth level compared to Bank Madina Syariah. This can be seen from the increase and the achivement of ZIS fundraising target which automatically affects ZIS fund distribution. Meanwhile Bank Madina Syariah’s growth level is not good yet since there is no target and the professional zakat applied does not really bind the taxpayers therefore the ZIS fund might decrease anytime.