The search box follows your brand from four colors: Brand, Accent, Background, and a derived Surface, all under Elevated › Site Search › Settings › Theme & Style › Color Theme. Set them once and the box, results, pills, and highlights derive their palette; flip on Override theme colors when you need per-element control.
Navigate to Elevated › Site Search › Settings and locate Color Theme inside Theme & Style.

Brand drives the primary accents, such as the active filter pill. Accent colors secondary highlights. Background sets the base surface, and Surface is derived from it automatically; the live preview shows every change before you save.
Click Save Settings, then check the box on the frontend:

For per-element control, switch on Override theme colors. It reveals individual color controls, pre-filled from the derived palette, covering the input, results area, pills, badges, and the Modern modal. Change only what needs changing; cleared fields fall back to the derived value.
If your agent is connected (see Connect Your AI Agent), you can skip the steps above:
Use my brand colors in Site Search: brand #0B5FFF and accent #16C79A.
The agent writes both colors in one settings update and reads the saved values back.
A color refuses to change. An override is set for that element. Check the controls revealed by Override theme colors; clearing a field returns it to the derived palette.
Contrast looks wrong after a color change. Adjust Background and check the preview; the derived Surface follows it, and dark backgrounds pair best with Dark mode (see How to Use Light and Dark Mode).