No, it will not kill beneficial microbes. Phosphoric acid is a potent and stable pH adjuster which means you won't need very much to correct pH and it will keep the pH in line longer than other pH adjusters like citric acid.

Can I use vinegar instead of pH down?

Currently, I use vinegar because it is easily accessible and is very cheap. Its aroumd $3 a bottle and last a full growing season. I mix a teaspoon of vinegar per gallon of water and to adjust the pH of my water from 7.5-7.8 to 6.2-6.5.

Can I use pH up and down in organic soil?

SaferGro pH Down is designed to quickly and effectively lower the pH in water into a more acidic range for use in organic, conventional and hydroponic growing. Unlike many pH adjusting products on the market; this product is non-hazardous and can be used in organic production.