The Food and Agricultural Organization estimates a 17% loss in the food production chain, making it imperative to adopt scientific and technological approaches to address this issue for sustainability. Industrial food production waste and its value-added applications, particularly in relation to a wide variety of pathogenic microorganisms and the health-related effects have not been thoroughly investigated. This study explores the potential of food production waste extracts—lemon peel (LP), hot trub (HT), and coffee silverskin (CSS) as sources of bioactive compounds. Extraction was conducted using hydro-methanolic extraction with yields in LP (482 mg/1 g) > HT (332 mg/1 g) > CSS (20 mg/1 g). The agar diffusion assay revealed the substantial antibacterial activity of all three extracts against Erwinia Amylovora, Escherichia coli, Bacillus subtilis, and Bacillus aquimaris. All extracts demonstrated activity against Gram-positive and Gram-negative bacteria, displaying minimum inhibitory concentrations effective against pathogenic bacteria like Listeria monocytogenes, Staphylococcus aureus, Vibrio parahaemolyticus, and Salmonella enterica. Total phenolic content (TPC in mg GAE/1g) was 100, 20, and 100 for CSS, HT, and LP, respectively. Antioxidant activity by ABTS indicated IC50 of 3.09, 13.09, and 2.61 for LP, HT, and CSS, respectively. Also, the antioxidant activity of the extracts was further confirmed by DPPH assay with the best activity in CSS (9.84 GAEg−1) and LP (9.77 mg of GAEg−1) rather than in HT (1.45 GAEg−1). No adverse cytotoxic effects on HaCaT cells were observed. Pancreatic amylase inhibition demonstrated antidiabetic potential, with LP showing the highest levels (92%). LC-MS characterization identified polyphenols as the main compounds in CSS, prenylated compounds in HT, and flavanols in LP. The findings imply the potential sustainable use of food production waste in industry.