Duckweed is a future food and a source of affordable protein that has the potential to replace animal protein. This study aims to formulate a bio-fertilizer consisting of mangrove-associated bacteria to boost the growth and protein of duckweeds as a sustainable approach to increase plant-based protein yields. The culture-depending technique was performed by using Aleksandrow agar, Pikovskaya’s agar, and Jensen agar to screen potassium-solubilizing bacteria, phosphate-solubilizing bacteria and nitrogen-fixing bacteria, respectively, from mangrove soil sediments. Mangrove-associated bacteria that are close to <i>Acinetobacter radioresistens</i>, <i>Brachybacterium paraconglomeratum</i>, and <i>Enterobacter cloacae</i>, which are known as nitrogen-fixing bacteria, <i>Klebsiella quasipneumoniae</i>, <i>Bacillus tropicus</i>, and <i>Paenibacillus pasadenensis</i> known as potassium-solubilizing bacteria, and <i>Bacillus cereus</i> and <i>Bacillus thuringiensis</i> known as phosphate-solubilizing bacteria were identified through 16S rRNA gene sequencing. After that, three sets of bio-fertilizers were randomly formulated. Each set consisted of nitrogen-fixing bacteria, potassium- and phosphate-solubilizing bacteria, as well as commercial compost as a carrier. These formulated bio-fertilizers were evaluated for plant growth promotion and protein production on duckweed plants under temperatures between 26 and 30°C. The results showed that each set of our formulated bio-fertilizer can increase the nitrogen (N), phosphorus (P), and potassium (K), duckweed growth, and protein content when compared to the control group. It indicates that bio-fertilizers formulated with mangrove-associated bacteria and high NPK contents could enhance the growth of duckweed as well as its protein content, which could supply our future plant-based protein sustainably.