In the current age of fast-changing climate, food security is increasingly challenged. Modern agriculture has to boost the crop productivity in order to meet the needs of a continuously growing world population while adopting sustainable production systems to protect the environment and the human health. Climate-Smart agriculture (CSA) is an integrated approach combining several sustainable farming methods to mitigate adverse climate patterns. Current management strategies by prospecting plant–microbiome interactions in biotic and abiotic stress alleviation have been adopted in CSA. Although plant microbiomes have been extensively used as biofertilizers/biostimulants and biopesticides to enhance crop productivity and ameliorate plant health in the climate change context, research trends in plant–microbiome biotechnology are pointing out some shortcomings to be considered. More intensive research is still needed for better knowledge of the interactions prevailing within the trio plant–microbiome–environment to enhance the efficiency of microbial uses in CSA.