Agrochemicals are used for the past 70–80 years to protect crops and increase crop productivity. However, agrochemicals were reported to accelerate climate change by contributing to global GHG emission (approx. 24%). Since food insecurity, climate change, and sustainability are the major challenges of the current era, different studies have been done to address these challenges. Studies were conducted on plant-microbe interactions to identify microbes with traits useful to sustainable agriculture. One group of microorganisms called endophytes has been discovered which mediates plant fitness and productivity through the alleviation of abiotic and biotic stressors. Fitness traits are essential to plant productivity but difficult to introduce during breeding programs. This can be complemented by harnessing endophytes as they confer multiple traits for host plant fitness and productivity. Metagenomics-based endophyte study unraveled the genes and biomolecules involved in the fitness of plants and paved a way to engineer plant microbiomes suitable to a particular crop development. Endophyte-treated seeds showed faster germination and high photosynthetic rate than seeds left untreated, and bio-fertilizer-treated crops also show better performance and yields (15–37%) than crops treated with agrochemicals. Hence, endophyte contribution to food security and climate action should not be undermined. The aim of this review article is to show the potential application of microbial endophytes to sustainable agriculture, environment, climate change adaptation and mitigation, bioprospections, and limitations and gaps to expand endophytes application to greener agriculture and environment. The review used available literature sources publications showing the promises and opportunities of endophytes research for research and development.