Watermelon, Citrullus lanatus (Thunb.) Matsum. & Nakai, crops are continuously exposed to soilborne diseases. In many areas of the United States, greenhouse-raised watermelon seedlings are transplanted to the field to allow for early crop establishment and early fruit production. This practice can result in weakened root systems, which potentially make the plant prone to premature senescence and reduce crop productivity. Mycorrhizal fungi have been reported to improve plant growth in many crops through enhanced root growth and function. We hypothesized that amending potting mixes with commercial inocula of mycorrhizal fungi during seeding of watermelon in a greenhouse would improve watermelon production when seedlings were transplanted to the field. Colonization of watermelon roots with mycorrhizal fungi from three commercial formulations was compared with the colonization of onion roots to confirm the efficacy of the mycorrhizae. Two inocula of mycorrhizal fungi that resulted in colonization of watermelon roots were tested in the field and glasshouse for their potential to improve watermelon production. MycoApply improved early plant growth in two tests, one under Meloidogyne incognita-infested conditions in loamy sand and another at two phosphorus fertilizer levels (0 or 22 kg·ha−1 P) in a loam soil. Mycor Vam Mini plug improved early fruit yield in soil infested with M. incognita. Application of Myconate (formononetin), a potential enhancer of colonization with mycorrhizae, increased early fruit yield in M. incognita-infested soil. Myconate had positive effects when potting mixes were not amended with inoculum of mycorrhizal fungi, but reduced watermelon growth when mycorrhizal fungi were supplied in the potting mix. In glasshouse tests, inoculation with mycorrhizal fungi did not suppress disease. Mycorrhizal fungi inoculations improved early plant establishment and increased the most valuable early fruit yield under some environmental stress conditions but did not increase total fruit yields.