Libidibia ferrea Mart, belonging to the Fabacee family, is a medicinal plant known for its biological properties and production of phenolic compounds. Previous studies reveal the biological activity of its phenolic constituents, making it very promising for the development of new medicines. Seasonality and geographic distribution of species can modify the production of secondary metabolites in Fabaceae species in terms of the preferentially activated metabolic pathways and, consequently, interfere with the medicinal properties of these species. Studying the influence of seasonality on the production of phenolic constituents is essential to establish conditions for “cultivation,” species collection, standardization, production, and safety in traditional medicine. This unprecedented study proposed to evaluate the influence of seasonal variations and habitat on the production of phenolic compounds and biological properties of the ethanolic extracts of the stem bark from L. ferrea, whose specimens were collected from the Caatinga and the Atlantic Forest, biomes of Brazil. Antimicrobial activity was determined by broth microdilution. Cytotoxicity was evaluated through a colorimetric assay using MTT. ABTS and DPPH radical reduction methods estimated antioxidant capacities. Folin-Ciocalteu and AlCl3 spectrophotometric methods quantified total phenolics and flavonoids, respectively. In turn, radial diffusion quantified tannin content. PCA score plot and HCA dendogram were obtained by multivariate analysis of 1H NMR data. The cytotoxicity against C6 glioma cells was observed only for Atlantic Forest extracts (EC50 = 0.13–0.5 mg mL−1). These extracts also showed selectivity against Gram-positive bacteria Bacillus subtilis (ATCC 6633) [MICs 500–2000 μg mL−1], B. cereus CCT 0096) [MIC = 250 μg mL−1], Staphylococcus aureus (ATCC 6538) [MICs = 250–500 μg mL−1], S. epidermidis (ATCC 12228) [62.5–1000 μg mL−1], mainly to Staphylococcus sp. Caatinga extracts showed higher production of flavonoids and antioxidants in the summer [7.36 ± 0.19 μg QE mg−1 extract; IC50ABTS = 4.86 ± 0.05 μg mL−1], spring [5.96 ± 0.10 μg QE mg−1 extract; IC50ABTS = 5.96 ± 0.08 μg mL−1 ], winter [4.89 ± 0.25 μg QE mg−1 extract; IC50ABTS = 6.72 ± 0.08 μg mL−1 ]. Regarding habitat, two discriminating compound patterns in the studied biomes were revealed by NMR. The results indicated that the Caatinga biome offers better conditions for activating the production of phenolics [336.34 ± 18.1 μgGAE mg−1 extract], tannins [328.38 ± 30.19 μgTAE mg−1 extract] in the summer and flavonoids in winter, spring, and summer. The extracts that showed the best antioxidant activities were also those from the Caatinga. In turn, extracts from the Atlantic Forest are more promising for discovering antibacterial compounds against Staphylococcus sp and cytotoxic for C6 glioma cells. These findings corroborated the traditional use of L. ferrea bark powder for treating skin wounds and suggest the cytotoxic potential of these extracts for glioblastoma cell lines.