To overcome abiotic stress such as high salinity or drought, plants will synthesise specific metabolites to enhance the tolerance level. These metabolites are used as markers to relate to the potential metabolite pathways to alleviate salinity or drought stress with enhanced tolerance. The application of plant growth-promoting bacteria (PGPB) is of high potential in reducing the symptoms induced under salinity or drought stress. However, limited studies have reported on the potential metabolite markers to represent the relationship between PGPB and plants to alleviate the salinity or drought stress. This review aims to summarise and develop a novel metabolite framework to relate the potential metabolite markers synthesised under salinity or drought stress as induced by PGPB. The metabolite framework is built based on a range of PGPB-induced metabolite markers modulated in different plants for stress alleviation and growth enhancement. From this review, major metabolite markers induced by PGPB under salinity and drought stress were identified as amino acids (ethylene, indole-3-acetic acid, salicylic acid, and proline) and isoprenoid (abscisic acid) in different plants. This framework is vital for constructing the metabolite network to decipher the underlying mechanisms for PGPB to enhance the tolerance of plants under salinity or drought stress in the future.