Climate change is the most prevalent issue in the last decades and is likely to accelerate due to anthropogenic factors. One of the most prominent contributors to climate change is the agricultural sector, which includes the release of greenhouse gases, large volumes of organic agro-waste, and deforestation, to name a few. The industry itself is also heavily impacted, as plants are sensitive to slight environmental changes, which include increases in temperature and CO2, drought, altered nutrient availability in the soil, and xenobiotics. The impact of climate change and unregulated agroecosystems can be categorized as direct and indirect, particularly concerning microbial diversity. The consequences include changes in environmental conditions that affect the soil microbiome of crops, ultimately decreasing productivity and yield. Microbes are essential for nutrient acquisition from the soil, maintaining soil health and biodiversity, and helping in biocontrol along with bioremediation of the soil. The microbes not only fulfil the criteria of a biofertilizer but also increase resistance against diseases by maintaining a healthy soil microbiome. Biofertilizers in agroecosystems are increasingly growing as they put less strain on the soil microbial community than synthetic fertilizers. Recent technological advancements like metaproteomics, metatranscriptomics, metabolomics, and novel gene-altering methods have significantly improved our understanding of the role of the microbiome in crop improvement and development. Rhizosphere engineering has shown promising results in improving crop yields and productivity. However, a deeper understanding of dynamics in microbial diversity and plant–microbe interaction in agroecosystems is essential to keep up with the changing climate. Advancing research in this field, with a focus on the role of microbial diversity in enhancing plant growth and resistance against diseases using advanced technologies, is crucial in developing sustainable agricultural practices that are better equipped to adapt to an evolving climate.