Transition metal catalysts play a vital role in a wide range of industrial organic processes. The large-scale production of chemicals relying on catalyzed organic reactions represents a sustainable approach to supply society with end products for many daily life applications. Homogeneous (mainly for academic uses) and heterogeneous (crucial in industrial processes) metal-based catalysts have been developed for a plethora of organic reactions. The search for more sustainable strategies has led to the development of a countless number of metal-supported catalysts, nanosystems, and electrochemical and photochemical catalysts. In this work, although a vast number of transition metals can be used in this context, special attention is devoted to Ir- and Pd-based catalysts in the industrial manufacture of pharmaceutical drugs. Pd is by far the most widely used and versatile catalyst not only in academia but also in industry. Moreover, Ir-based complexes have emerged as attractive catalysts, particularly in asymmetric hydrogenation reactions. Ir- and Pd-based asymmetric reductions, aminations, cross-coupling reactions, and C–H activation are covered herein in the production of biologically active compounds or precursors; adaptation to bulk conditions is particularly highlighted.