Background Bixa orellana L. is a plant native to Brazil but grows in other parts of the world including Bangladesh. This plant has been used for many years by indigenous people around the globe for a variety of applications. In Bangladesh, it is known as Doigota and the plant is underutilized and reported endangered. The present study aimed to perform comparative profiling where aqueous, ethanolic, and methanolic extracts of the seed, branch, and leaf of B. orellana plants were investigated for in vitro phytochemicals, antioxidant, and antibacterial activities. Results Phytochemical screening indicated the presence of nine different phytochemicals in varying degrees, which suggests the chemical diversity of this plant. Quantification of phenolics, flavonoids, and tannins was performed where leaf extracts contained significantly higher quantities of these phytochemicals than extracts from seed and branch. The highest phenolics (186.02 mg/g) were found in the methanolic extract of the leaf, whereas the highest flavonoids (61.01 mg/g) and tannins (36.74 mg/g) were found in aqueous extract of the leaf. Antioxidant activity has been evaluated by DPPH scavenging assay where the aqueous extract of leaf showed 93.62% scavenging activity at 800 μg/mL extract concentration. Although the extracts prevented the growth of both Gram-positive and Gram-negative bacteria, the antibacterial activity (zone of inhibition) of aqueous and methanolic extracts of the leaves were higher than those of the seed and branch extracts against Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria, respectively. Conclusions We found that B. orellana leaf extracts possess the highest antibacterial activities. The extracts had significant antioxidant and free radical-scavenging activities. The antioxidant and antibacterial activities could be attributed to high flavonoid and phenolic contents. These results suggest that the extracts of B. orellana possess bioactive compounds that could be used for different purposes such as source of new antibiotics or alternative natural preservatives in food matrices due to mainly their antioxidant and antibacterial activities.