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ESA's interplanetary missions Rosetta, Mars Express and VenusExpress have common on-board software, which includes an On-board Control Procedure (OBCP) execution system. These OBCPs are managed on-board as binary files stored in the Mass Memory and in the central computer RAM, possibly in several copies for redundancy purposes. On ground, the source files and compiled output have historically been stored in a variety of places, from version control tools to shared network drives. Jointly the missions identified a need to consolidate into a unified system, capable of supporting the different approaches to OBCPs as adopted by each mission. In parallel to the configuration management aspects, the development of new OBCPs has migrated to a procedure-based methodology which allows OBCP creation in a manner more consistent with the procedure development interface more familiar to ground controllers . The intention is for spacecraft operations engineers to be able to generate new OBCPs without any particular programming skill. Although developable without software background, the OBCPs represent modifications to spacecraft on-board autonomy with major function and potentially critical impact. Thus the new configuration management system needs to integrate with the procedure generation tool and enable rapid end-to-end development while maintaining strict version control as required by onboard software. This paper presents the requirements derived for such a multi-mission system, the implemented solution common to the ESA planetary missions, and lessons learned.