The biochemical composition, secondary metabolites (phenolic compounds, flavonoids) and antimicrobial potential of different varieties of Emirati date (Phoenix dactylifera L.) pits were investigated. Total phenolic acids (TPC) and total flavonoid contents (TFC) of the different date pits were measured using a Folin–Ciocalteau reagent. Different organic solvents [(n-hexane; H2O: EtOH (1:1); ethyl acetate; acetone: Water (1:1); and methanol: Chloroform (1:1)] were compared to evaluate the phytotoxicity of Ajwa, Fard, Khalas, Khodari, Abu Maan, Lulu, and Mabroom date pits. The antimicrobial activity of the date pit extracts were evaluated by means of agar-well diffusion assay on Staphylococcus aureus (ATCC 29123), Escherichia coli (ATCC 25922) and Candida albicans (ATCC 66027). Minimum inhibitory concentrations (MICs) were measured following clinical laboratory standardization institute (CLSI) protocol. The biochemical analyses of date pits indicate that TPC were ranged from 7.80 mg of equivalent gallic acid⁄100 g dry weight in Ajwa to 4.65 mg in Mabroom. The TFC were ranged between 1.6–4.54 mg of equivalent catechin⁄100 g dry weight. Ajwa pit extract showed good quality traits (higher protein, lower ash content, and intermediate dietary fiber). The results indicate that the ethyl acetate extract of Khalas and Khodari inhibited S. aureus with an inhibition zone diameter of 20 mm and MIC of 10 mg/mL. Abu Mann pit extract inhibited the S. aureus and also decreased the population of E. coli. The diameter of inhibition zone was 15, 16, and 18 mm after treatment with Ajwa extracts, while the MICs were 7.5 and 5 mg/mL. The MeOH: CFM extract of Abu Mann and Ajwa was more potent against E. coli bacteria than any other extract. This work demonstrates that the Emirati date pits extract has antimicrobial (antibacterial, antifungal) potential and can be used as phytotoxic natural compounds.