Desert plants survive under extreme environmental conditions with the support of microbial symbionts that enhance host drought tolerance through diverse mechanisms, representing a valuable resource for improving crop resilience in arid regions. This study aimed to isolate and characterize plant growth-promoting bacteria (PGPB) from the roots of the desert shrub Encelia farinosa, grown in Colorado Desert soil under controlled glasshouse conditions (25 °C for three months). Bacterial isolates were obtained from root samples and identified via 16S rRNA gene sequencing. A total of more than 1,800 colonies were initially cultured, from which 84 genetically distinct isolates representing 41 genera and 56 species were selected for comprehensive phenotypic screening. Each isolate was assessed for seven key PGP traits: phosphate solubilization, siderophore production, indole-3-acetic acid (IAA) synthesis, growth on nitrogen-free media, ACC deaminase activity, and extracellular protease and amylase production. Screening revealed widespread PGP functionality: 33% of isolates solubilized phosphate, 65% produced IAA, 23% produced siderophores, 41% grew on nitrogen-free media, 25% showed ACC deaminase activity, 53% produced protease, and 56% produced amylase. Notably, nine isolates (11%) belonging to the genera Paenibacillus, Agrobacterium, Rhizobium, Bacillus, Cellulomonas, Agromyces, and Pseudomonas exhibited five or more PGP traits simultaneously. These genetically diverse, multifunctional desert bacteria represent promising candidates for developing microbial inoculants to enhance crop stress tolerance in dryland agriculture.