Embodiments of the present invention address deficiencies of the art in respect to applying user configurable options during bootstrap and provide a novel and non-obvious method, system and computer program product for user selectable configuration options application for inaccessible nonvolatile storage at bootstrap. In one embodiment of the invention, a method for user selectable configuration options application for inaccessible nonvolatile storage at bootstrap can be provided. The method can include powering up a motherboard for a computer system and reading user selectable configuration options for the computing system from sticky bits prior to bootstrap for the motherboard. The method further can include applying the user selectable configuration options to the computing system. Finally, the method can include performing bootstrap for the motherboard subsequent to applying the user selectable configuration options.