World population is projected to reach almost ten billion by 2050, approximately 24% more than today. This situation leads to a pressing need to increase crop production and yields, but not at any cost: it must be done minimizing environmental damage and, consequently, also harms to human health. Trying to achieve this goal, the European Union (EU)’s Green Deal has as one of its objectives for the present decade to reduce the application of chemical inputs in agriculture. This fact creates the need to search for organic alternatives, gaining importance at this point plant growth promoting microorganisms (PGPM) and their metabolites. Within this group, plant growth promoting fungi (PGPF) such as endophytes or arbuscular mycorrhizae, are particularly important. Among endophytes, the genera Trichoderma, Penicillium, or Aspergillus have been intensively studied with this purpose, whereas within arbuscular mycorrhizae, the genera Glomus and Rhizophagus are the most prominent. Both groups have the ability to generate specific secondary metabolites with plant-growth promoting activity in many crops, such as phytohormones, non-ribosomal peptides, poliketides, terpenes and alkaloids. The production, commercialization, and application of PGPF and their metabolites may be relatively simple and cost-effective. Consequently, they may represent a feasible organic alternative to replace many of the current synthetic fertilizers.