The LEGRI Science Operation Center (SOC) is the single contact point between the MINISAT-01 Centro de Operaciones Científicas (COC) located at Villafranca del Castillo (Madrid) and the LEGRI Consortium. Its architecture, operational procedures and associated software has been developed at the Universities of Valencia and Birmingham on the scope to define a integrated Data Analysis System, able to perform the daily follow-up of the instrument health, raw data files decompression and archiving activities (on-line and historical). Pointing and telecommand files generation is also a SOC responsibility. The aim of this paper is to report the SOC activities during the two years of LEGRI operations. Conclusions about the SOC architecture and procedures evolution on how to handle the operations for space-borne instrumentation, are also presented. Special attention has been paid to the operative evaluation of the pointing reconstruction solutions from the MINISAT-01 Attitude Control System by comparing them with those obtained with the LEGRI Star Sensor. The analysis of one year of observations shows the good agreement between both sets of data. No systematic deviations have been found with an averaged standard deviation of 1 degree in alpha and delta coordinates. For most of the time the MINISAT pointing system is working slightly better than expected and within specifications.