The oxidation of bio-based molecules in general, and of carbohydrates and furanics in particular, is a highly attractive process. The catalytic conversion of renewable compounds is of high importance. Acids and other chemical intermediates issued from oxidation processes have many applications related, especially, to food and detergents, as well as to pharmaceutics, cosmetics, and the chemical industry. Until now, the oxidation of sugars, furfural, or 5-hydroxymethylfurfural has been mainly conducted through biochemical processes or with strong inorganic oxidants. The use of these processes very often presents many disadvantages, especially regarding products separation and selectivity control. Generally, the oxidation is performed in batch conditions using an appropriate catalyst and a basic aqueous solution (pH 7–9), while bubbling oxygen or air through the slurry. However, there is a renewed interest in working in base-free conditions to avoid the production of salts. Actually, this gives direct access to different acids or diacids without laborious product purification steps. This review focuses on processes applying gold-based catalysts, and on the catalytic properties of these systems in the base-free oxidation of important compounds: C5–C6 sugars, furfural, and 5-hydroxymethylfurfural. A better understanding of the chemical and physical properties of the catalysts and of the operating conditions applied in the oxidation reactions is essential. For this reason, in this review we put emphasis on these most impacting factors.