Nowadays, getting a more environmentally sustainable cement production is one of the main goals of the cement industry. In this regard, the use of active additions, like fly ash and ground granulated blast-furnace slag, has become very popular. The behaviour, in the short-term, of cement-based materials with those additions is well-known when their hardening is produced under optimum conditions. However, real structures are exposed to different environments during long periods, which could affect the development of microstructures and the service properties of cementitious materials. The objective of this work is to analyse the effects in the long-term (up to 5 years approximately) produced by the exposure to different non-optimum laboratory conditions in the microstructure, mechanical and durability properties of mortars made with slag and fly ash commercial cements. Their performance was compared to that observed for ordinary Portland cement (OPC) mortars. The microstructure has been analysed using mercury intrusion porosimetry. The effective porosity, the capillary suction coefficient, the chloride migration coefficient and mechanical strengths were analysed too. According to the results, mortars prepared using slag and fly ash sustainable commercial cements, exposed to non-optimum conditions, show a good performance after 5-years hardening period, similar or even better than OPC mortars.