In this work, we study the preparation, structural characterization, and electrocatalytic analysis of robust Pt and Pd-containing catalyst structures for silicon-based formic acid micro fuel cells. The catalyst structures studied were prepared and incorporated into the silicon fuel cells by a post CMOS-compatible process of electrodeposition, as opposed to the more common introduction of nanoparticle-based catalyst by ink painting. Robust, high surface area, catalyst structures consisting of pure Pt, pure Pd, and Pt/Pd = 1:1 were obtained. In addition, Pt/Pd catalyst structures were obtained via spontaneous deposition on the electrodeposited pure Pt structure. The catalyst structures were characterized electrochemically using cyclic voltammetry and chronoamperometry. All Pd-containing catalyst structures facilitate formic acid oxidation at the lower potentials and deliver higher oxidation currents compared to pure Pt catalyst structures. Fuel cells of these catalyst structures show that pure Pd catalyst structures on the anode exhibit the highest peak power density, i.e. as high as 28.0 mW/cm2. The MEMS compatible way of catalyst electrodeposition and integration presented here has yielded catalyst structures that are highly active towards formic acid oxidation and are sufficiently robust to be compatible with post-CMOS processing.