Very large amount of microbialites, up to 70% of the reef volume takes part in the edification of Lower Bajocian coral reefs in the Chargey-lès-Port quarry (Haute-Saône, France). Such high amounts of microbialites were unknown within bioconstructions of Middle Jurassic age. Along the 16 m-thick section, seven successive biohermal or biostromal units developed on a shallow platform. Bioconstructions display a first coral growth phase with either constratal or superstratal growth fabrics. Coral fauna is relatively poorly diversified and is dominated by massive forms (Isastrea, Thamnasteria, and Periseris) or branched phaceloid (Cladophyllia) and ramose (Dendraraea) colonies. Corals can be heavily encrusted by microbialites of diverse forms and fabrics (leiolitic, thrombolitic, and stromatolitic). According to the coral growth fabrics, microbialite crusts developed on top of or at the underside of coral colonies, forming a coral-microbialite elementary unit. Microbialites show a multiphase development: (i) directly at the coral surface, a first and mm-scale microbialite layer locally developed; (ii) a second, cm-scale microbialite layer (up to 8 cm thick) covered the entire coral reef framework and assumed the main building role; and (iii) a third, mm- to cm-scale, laminated microbialite layer may also be observed onlapping previous reef structures, before having been progressively buried under sediments. Contemporaneously to the coral growth phase, the first microbialite layer developed on dead portions of coral colonies. The transition between coral growth and microbialite development (i.e., second layer of microbialites) is interpreted as a result of a coral reef crisis, probably reflecting more nutrient-rich conditions. The passage to a stromatolitic (third) layer suggests a control of the accumulation rate. Composition and architecture of coral-microbialite reef units of Chargey-lès-Port highlight the relations between high-frequency fluctuating environmental factors (mainly accumulation rate and trophic conditions) and reef development.