Apparatus and operating methods are provided for controlled atmosphere furnace systems. In one possible embodiment, hydrogen is injected from a hydrogen source to an enclosure. The hydrogen is circulated within the enclosure from a gas inlet to a gas outlet. A temperature is raised within the enclosure to a predetermined threshold. Hydrogen is pumped from the gas outlet to the gas inlet with an electrochemical hydrogen pump. The electrochemical hydrogen pump has a first electrode in fluid communication with the gas outlet, and a second electrode in fluid communication with the gas inlet. An electrical potential is provided between the first and second electrodes, wherein the first electrode has a higher electrical potential with respect to zero than the second electrode. Various methods, features and system configurations are discussed.