Marine sediments represent a valuable source for critical minerals that prompts growing research interest in their potential for sustainable resource recovery. This study investigated the impact of bioleaching microorganisms, evaluating three different microbial inocula: sediment indigenous Fe-oxidizing bacteria, sediment indigenous Fe- and S-oxidizing bacteria, and Acidhiobacillus ferrooxidans. Key operational parameters including initial pH (2.0–7.0), energy source (Fe and S), and total solids content (5–10%) were also tested to optimize bioleaching efficiency. The use of Fe- and S-oxidizing bacteria enriched from the marine sediment resulted in the highest bioleaching potential for all target critical minerals. Highest Al leaching (806 mg/L) was obtained an initial pH of 2.0 and TS of 10%, in the presence of added Fe and S, while highest K leaching (169 mg/L) was achieved under the same initial pH and TS, but in the absence of Fe and S. Conversely, Mg leaching was highest as 506 mg/L at an initial pH 2.0 and TS of 10% with the addition of Fe and S. Alicyclobacillaceae was one of the key dominant microorganisms in the microbial community during the bioleaching process. On the other hand, Sulfurifustis played a key role in the early shifts in the microbial community. Additionally, Least Square Boosting (LSBoost), Random Forest Regression (RF), and Linear Regression (LR) were evaluated for predicting critical mineral release, with LSBoost achieving highest R2 values.