<p><i>Ganoderma</i> sp. 1962 is an Amazonian isolate with reported potential for the production of bioactive compounds; however, the effects of specific submerged fermentation parameters on mycelial architecture and on the recovery and bioactivity of protein extracts remain poorly understood. In this study, the influence of different submerged fermentation conditions on the recovery of antioxidant proteins from <i>Ganoderma</i> sp. 1962 was evaluated. Molecular identification was performed by sequencing the internal transcribed spacer (ITS) region followed by phylogenetic analysis. The isolate was cultivated under four nutrient compositions combined with agitated (A) and non-agitated (NA) regimes, resulting in eight experimental conditions. Mycelial biomass was structurally characterized using Scanning Electron Microscopy (SEM) and Attenuated Total Reflection–Fourier Transform Infrared (FTIR-ATR) spectroscopy. Protein extracts obtained from the mycelial biomass were analyzed for soluble protein content, total phenolic compounds (TPC), and reducing sugars (RS). Antioxidant activity was assessed using ABTS^•+, DPPH^•, metal chelating ability, and reducing power assays. BLAST analysis of ITS rDNA sequences revealed high similarity (&gt; 98% identity) to <i>Ganoderma multiplicatum</i>, which was subsequently confirmed by phylogenetic analysis using reference sequences from GenBank. Biomass production ranged from 5.57 to 8.73&#xa0;g L^− 1, with marked variation in glucose consumption among conditions and a stronger tendency toward pH acidification under agitated cultivation. Macromorphological differences were predominantly characterized by pellet formation under agitated cultivation and by mycelial aggregates under static conditions. Micromorphological analysis revealed cultivation-dependent traits, including the formation of short, highly branched “staghorn” hyphae under non-agitated conditions, whereas agitated cultures promoted long, filamentous hyphae. FTIR-ATR analysis showed significant spectral differences among samples, indicating that culture medium composition strongly influenced the chemical composition of the biomass. The E3NA condition (Experiment 3, non-agitated) yielded the highest soluble protein content (218.35 ± 16.95 mg g^− 1 extract), while E1A (Experiment 1, agitated) exhibited the highest levels of RS (25.50 ± 1.59 mg g^− 1 extract) and TPC (31.96 ± 1.39&#xa0;mg GAE g^− 1 extract). The E1A extract showed the strongest antioxidant activity, with values of 90.34 ± 0.66% (ABTS^•+), 68.09 ± 1.74% (DPPH^•), and 0.335 ± 0.011 (reducing power), suggesting that protein–phenol and protein–carbohydrate interactions may contribute to antioxidant activity, as supported by correlation analysis. Although non-agitated fermentation favored soluble protein recovery, protein–metabolite interactions may play a more relevant role in antioxidant activity. Overall, this study provides novel evidence of the potential of <i>G. multiplicatum</i> to produce antioxidant proteins under submerged fermentation.</p>