PROBLEM TO BE SOLVED: To provide a manufacturing method of seed vinegar made from seeds such as loquat seeds, which is good for the health.SOLUTION: The method includes the steps of: washing loquat seeds and then pulverizing the seeds into a granular form; immersing the granular loquat seeds in water and then steaming the granular loquat seeds; adding rice malt and water to the steamed granular loquat seeds and performing a saccharification treatment of the mixture; adding yeast to the solution obtained by the saccharification treatment so as to perform an alcoholic fermentation; adding stock vinegar to the solution so as to perform an acetic fermentation, on completion of the acetic fermentation step, squeezing the granular loquat seeds in the solution and separating the solid content such as the granular loquat seeds to filter the loquat seed vinegar liquid.