The Mugilidae are a group of fish with a great interest for aquaculture due to their omnivorous profile, rapid growth, and resistance to environmental variations. The selection of feed ingredients for these species is currently focused on an extensive use of plant by-products, with this being limited by their content in anti-nutritive factors (mainly phytate and non-starch polysaccharides; NSPs). Nevertheless, specific enzymes can be used to counteract some of those negative effects. In the present study, the effect of pretreating two high-plant feeds with a mixture of enzymes (glucanases + phytase) on the digestive use of protein and phosphorus by juvenile mullets (Mugil cephalus) was assessed using both in vitro and in vivo assays. The enzymatic treatment significantly modified the potential bioavailability of some nutrients, such as a reduction of sugars, pentoses, and phytic phosphorus. Also, it increased the digestibility of protein in one of the feeds but reduced that of phosphorus in both of them. The potential usefulness of enzyme treatment and the information provided by the two types of assays are discussed.