Soil salinization poses an important threat to terrestrial ecosystems and is expected to increase as a consequence of climate change and anthropogenic pressures. Conventional methods such as salt-leaching or application of soil amendments, or nature-based solutions (NBSs) such as phytoremediation, have been widely adopted with contrasting results. The use of cyanobacteria for improving soil conditions has emerged as a novel biotechnological tool for ecosystem restoration due to the unique features of these organisms, e.g., ability to fix carbon and nitrogen and promote soil stabilisation. Cyanobacteria distribute over a wide range of salt concentrations and several species can adapt to fluctuating salinity conditions. Their application in agricultural saline soil remediation has been demonstrated, mostly in laboratory studies, but there is a lack of research regarding their use in natural ecosystems restoration. In this article, we provide an overview of the current knowledge on cyanobacteria in the context of ecosystem restoration. Examples of the application of cyanobacteria in alleviating salt-stress in plants and soils are presented. Furthermore, we acknowledge gaps regarding the extensive application of cyanobacteria in salt-affected soils remediation and discuss the challenges of NBSs in salt-affected soils restoration.