Several preferences which relate to Gnumeric as a whole can be configured and will affect the appearance and behaviour of the program every time it is run. These preferences can be set by the user.

Gnumeric provides a main preference configuration panel which allows users to configure fundamental properties of the program including the font used within the spreadsheet, the type of file generated when a workbook is saved, default settings for the tools and the 'undo' mechanism, as well as several fundamental properties of the program, such as the pixel pitch of the display, which require advanced knowledge to understand. Section 13.2 ― General Preferences explains how to alter these preferences.

The toolbars can also be configured by being hidden from view. This allows Gnumeric to be fit into a smaller space. Section 13.3 ― Toolbars explains how to hide or show each toolbar.

Much of the functionality of Gnumeric is provided through the plugin mechanism. Individual plugins can be disabled to save memory space or when the plugin computer code is being altered. Section 13.4 ― Plugins explains how to disable and re-enable Gnumeric plugins.

Gnumeric is designed to be used around the globe and therefore allows the use to determine the language for the menus and to determine location specific information such as the character used to separate whole numbers from fractional units. These language and locale settings are explained in Section 13.5 ― Languages and Locales.