As agriculture and food security face unprecedented challenges, emerging agricultural innovations and existing practices require ongoing examination in the context of sustainability. In this review, we focus on the use of probiotic microorganisms for improved plant production. As plants are enormously diverse, emphasis is placed on the fundamental sites of plant-microbe interactions regarding benefits and challenges encountered when altering the microbiome of these locations. The soil, the external plant epidermis, and internal plant tissue are considered in discussion regarding the type of plant probiotic application. Plant probiotics range from broader soil beneficial microorganisms (such as Trichoderma spp.) through to specialised epiphytes and endophytes (such as root nodule bacteria). As each site of interaction affects plant growth differently, potential outcomes from the introduction of these exogenous microorganisms are discussed with regard to plant productivity. Finally, recommendations regarding regulation and future use of plant probiotics are points of consideration throughout this review.