Microporous and tight limestones, with contrasting porosity and permeability values directly related to the microfabric of the micritic matrix, outcrop in the Urgonian Formation of the French Jura Mountains. This study investigates the factors controlling the differentiation between the microporous and tight facies, and proposes a diagenetic model for the development and preservation of the microporosity in these limestones. The petrophysical properties are not related to the depositional texture, the petrographical content or the mineralogical composition. However, the tight layers contain indications of emersion (e.g.: bird eyes, keystone vugs, and desiccation cracks). The sedimentation in very shallow conditions up to emersion is confirmed by the covariant more positive values of oxygen and carbon isotopes. The microporous intervals systematically occur a few meters below the tight layers affected by emersion. This position strongly suggests the importance of meteoric water input rapidly after sedimentation in the differentiation between tight and microporous limestones. The diagenetic model proposed for the development and preservation of the microporous facies involves partial early cementation of the interstitial mud, mainly composed of low-Mg calcite crystals (sedimentation during a calcite sea period), inside a meteoric phreatic lens by in situ dissolution–reprecipitation processes (“hybrid Ostwald ripening”). This early cementation partly preserves the original microfabric and intercrystalline microporosity and allows the carbonate sediment to resist compaction during burial. The identification of the conditions favorable to the development of microporosity in these Urgonian limestones may improve the knowledge and modeling of some microporous carbonate reservoir rocks.