Background Global agriculture is undergoing a phase of agroecological transition. This transition will be characterized by adoption of agroecological cropping practices and by an increased diversity of soil management/tillage practices. However, very little is known as to whether or not crop seed germination and seedling emergence (hereafter referred to as SGE) will be affected under these cropping practices. Scope This paper first proposes a conceptual scheme which integrates key abiotic and biotic factors affecting crop SGE. Subsequently, the key mechanistic factors affecting SGE (i.e. intrinsic factors related to the seeds, and extrinsic factors related to the biotic and abiotic conditions of the seedbed), and how crop management practices can influence SGE through alterations of these direct mechanistic factors are discussed. This is done with special emphasis on how agricultural practices, particularly those related to agro-ecology, may impact SGE. Conclusions Crop SGE are affected by five major groups of drivers, namely seed and seedling characteristics, seedbed physical components, seedbed chemical components, seedbed biological components, and cropping systems. Although the crop SGE failure frequently occurs under field conditions, very little quantitative information is available in the literature on the real economic impact, the precise cause/s and ranking of factors associated with this failure. Re-seeding is often practiced for a number of crops to compensate the lack of SGE with significant direct and indirect costs for farmers. Little information exists in the literature concerning how SGE will be affected under agroecological cropping systems, such as conservation agriculture, or organic farming, or under climate-driven changes. Field observation, experimental and modeling studies are needed to fill the current knowledge gaps on the economic impact, precise cause/s and ranking of different stress factors associated with SGE failure.