The study improves the understanding of the basal part of the Eocene Seeb Formation of Oman, informally known as “Unit 1”, in terms of microfacies, lithostratigraphy and shale migration within the context of regional tectonics. We logged four sections bed-by-bed over a distance of 8.3 km, collected samples and analyzed thin-sections as well as XRD samples. For the first time, the microfacies and stratigraphic correlation of the lowermost part of the limestone-dominated Seeb Formation were studied in detail. In the analyzed area, Unit 1 is ~20 to 40 m thick, with the thickness increasing to the SE. In the upper part of Unit 1 is a laterally continuous shale horizon. The limestones of Unit 1 contain mostly packstones and grainstones. The dominant standard microfacies types are SMF 18-FOR and SMF 16. The former is dominated by benthic foraminifera, and the latter by peloids. Both SMFs indicate restricted lagoonal conditions. Foraminifera are common in Unit 1 and indicate a middle Eocene age. Considering the abundance of encountered foraminiferal bioclasts, it appears probable that the lagoon barrier was mainly composed of foraminiferal tests. Gutter casts, slumps and debrites indicate an active, partly unstable syndepositional slope, which was likely initially created by uplift of the Saih Hatat Dome and Jabal Nakhl Subdome. Differential regional uplift due to a more pronounced overall doming in the NW (Jabal Nakhl Subdome) than in the SE (Saih Hatat Dome) explains more accommodation space and greater thickness towards the SE. For the first time, we report visco-plastic shale migration/intrusion within the Seeb Formation, related to a shale horizon of Unit 1. This shale locally migrated as indicated by (1) local thickness variations, (2) detached limestone boulders floating in the shale, (3) limestone beds that have been cut-off by the shale and (4) dragged by the shale (5) an upward shale intrusion/injection which then spread parallelly to bedding similar to a salt tongue and (6) tilting overlying limestones. We suggest that shale migration is related to post-“mid”-Eocene E-W convergence between Arabia and India and to faulting or to the second, late Paleogene/early Neogene, faulting interval of the Frontal Range Fault. The shale horizon in the upper part of Unit 1 is a marker bed, which can be correlated across the study area.