Currently, no curative treatments exist for most neurological disorders. Nevertheless, the involvement of the gut microbiota has gained increasing interest over the last years. In this review, we summarize the main findings published between April 2019 and March 2020 that are related to the use of microbiota-modulating agents to treat depression, Alzheimer’s disease (AD), and Parkinson’s disease (PD). These ‘psychobiotics’ were investigated individually or in combination and included probiotics (e.g., Bifidobacterium and Lactobacillus strains), prebiotics (e.g., polysaccharides and plant extracts), medicinal products (e.g., antidepressants and vitamins), as well as physical activity or infrared red-light treatment. All agents improved disease-related abnormalities to some extent. Their main effects involved the restoration of gut homeostasis by altering gut microbiota composition and suppressing intestinal inflammation. Disease symptoms improved associated with a reduction in cytokine levels, microglia activation, plaque deposition and neuronal cell death and with an increase in neurotrophic factors and glucose uptake in the brain. Furthermore, the 5-HT, TLR, NLRP3 and PPARʏ signaling pathways were highlighted as major bidirectional communication routes between the gut and the brain. In addition, whereas Bifidobacterium longum, Bifidobacterium lactis and Lactobacillus plantarum improved the symptom severity and affected pathophysiological pathways of both depression and AD, Lactobacillus rhamnosus and Lactobacillus acidophilus were shown to ameliorate PD as well as depression or AD. Although most studies have been performed in animal models and the exact underlying mechanisms and pathways need further investigation, influencing the microbiota-gut-brain communication has major potential for the future treatment of depression, AD and PD.