Halophytes are considered emerging functional foods as they are high in protein, minerals, and trace elements, although studies investigating halophyte digestibility, bioaccessibility, and intestinal absorption are limited. Therefore, this study investigated the in vitro protein digestibility, bioaccessibility and intestinal absorption of minerals and trace elements in saltbush and samphire, two important Australian indigenous halophytes. The total amino acid contents of samphire and saltbush were 42.5 and 87.3 mg/g DW, and even though saltbush had a higher total protein content overall, the in vitro digestibility of samphire protein was higher than the saltbush protein. The in vitro bioaccessibility of Mg, Fe, and Zn was higher in freeze-dried halophyte powder compared to the halophyte test food, suggesting that the food matrix has a significant impact on mineral and trace element bioaccessibility. However, the samphire test food digesta had the highest intestinal Fe absorption rate, whereas the saltbush digesta exhibited the lowest (37.7 vs. 8.9 ng/mL ferritin). The present study provides crucial data about the digestive “fate” of halophyte protein, minerals, and trace elements and increases the understanding of these underutilized indigenous edible plants as future functional foods.