The human microbiome, or the plethora of microorganisms symbiotically coexisting with us, plays a crucial role in both the health and the disease of the host. Interestingly, the gut microbiome has been identified as unique and characteristic to any human being, with common functionalities, even common evolutionary trends with age. A stable, rich, and diverse gut microbiome has been associated to a healthy intestinal state and clinical outcome, thus unbalanced gut microbial composition (i.e., dysbiosis) has been associated with detrimental outcomes, such as inflammation or altered metabolism. To reverse the negative effects of dysbiotic microbiome, fecal microbial transplantation (FMT) has been proposed as a successful strategy (initially demonstrated for Clostridioides difficile recurrent infections). However, several attempts have been performed to use FMT to overcome other recalcitrant dysbiotic situations, especially for the case of inflammatory bowel diseases (IBD). In this sense, supportive data are scarce and focused mainly in ulcerative colitis where some early results set a trend toward some clinical effect. Nonetheless, before FMT may be supported for its extensive use in clinics, besides more robust studies, there is a need to standardize and optimize the procedure with special attention to the matching of donor/recipient. We review current state of the art in FMT in the IBD clinical field with special attention to donor selection, FMT preparation, and patient matching.