In late 2009, CO₂ and CH₄ observations were initiated with a Wavelength-Scanned Cavity Ringdown Spectrometer (CRDS) which records data in the Hz range. Due to its superior precision and the full temporal coverage, the CRDS instrument became the master instrument for CH4 observations while the GC-FID/ECD system was operated until summer 2016 to ensure a seamless transition and for quality control purposes. The CRDS model for CO2 and CH4 was replaced in September 2011 by a newer CRDS model being capable to measure CO₂, CH₄ and CO. Since January 2012, the data recorded with CRDS are also used as the primary CO time series.

Observations were initially coupled to an upstream installed custom-built calibration/drying unit. The sample air was dried prior to analysis by means of a Nafion dryer until August 2010. Along with CO₂ and CH₄, the instrument is also capable to measure water vapour. Thus, the greenhouse gas data can be corrected for interferences of remaining water traces. From August 2010 onwards, no water vapour removal was used anymore and CO₂ and CH₄ dry air mixing ratios were determined by application of an empirical humidity correction to the fully unaltered humid gas stream accounting for dilution and pressure broadening effects. When the CO₂/CH₄/H₂O analyser was replaced by the four-channel (CO₂/CH₄/CO/H₂O) analyser in September 2011, the sample air was again dried prior to analysis, mainly to improve performance of the CO observations.

In December 2014, the measurements were complemented by high-resolution, continuous N₂O measurements. To do so, Empa started operating an off-axis integrated cavity output spectrometer (OA-ICOS) along with a commercially available multi-inlet unit with custom-made modifications used for calibration next to the GC-FID/ECD system. The superior precision and the continuous operation of the OA-ICOS compared to GC-ECD allow measuring short-term N₂O variations that could not be detected with gas chromatography before. The laser spectrometer is also capable of measuring CO and H₂O with high precision. Similar to the CRDS operation, dry air mole fractions can be determined by applying a humidity correction to the fully unaltered humid gas stream accounting for dilution and spectroscopic effects. Side-by-side N₂O measurements with GC-ECD and OA-ICOS were performed until summer 2016 when the GC-ECD was dismantled. The OA-ICOS observations needed to be stopped in November 2019 due to severe instrumental issues.

N₂O measurements were resumed with a new Cavity Ringdown Spectrometer (CRDS), equipped with an upstream permeation dryer and a custom-built calibration unit in August 2020. Since 2016, the CO₂, CH₄, CO and N₂O observations also became part of the European Integrated Carbon Observation System (ICOS) Research Infrastructure. ICOS aims at providing long-term observations of greenhouse gas fluxes from ecosystems and the oceans, and greenhouse gas concentrations in the atmosphere. To do so, harmonized operation procedures were developed and the CO₂, CH₄, CO and N₂O observations at Jungfraujoch take advantage of considerable synergies. Central facilities were established for sensor evaluation, development of processing algorithms, to support and harmonize the observations, for quality control and data analysis as well as to gather all data in a central database and to ease data dissemination. Next to the atmospheric greenhouse gas observations at Jungfraujoch, the ICOS-CH consortium also contributes data from the ecosystem station Davos to the ICOS Research Infrastructure.

The three greenhouse gases CO₂, CH₄, and N₂O do all show a positive trend at Jungfraujoch, in agreement with other global observations at remote locations. The positive trends can be explained by the excessive emissions of these long-lived species due to anthropogenic activities like the combustion of fossil fuels, and agricultural practives like rice cultivation, fertilizer applications, and ruminants farming. The positive CO₂ trend is overlain by a pronounced seasonal cycle which is due to the dominance of photosynthetic CO2 uptake by vegetation in summer. Due to the higher reactivity of carbon monoxide and, thus, the shorter residence time of CO in the atmosphere, CO concentrations at Jungfraujoch are largely driven by European processes. CO is mainly emitted by incomplete combustion. Improvements in the efficiency, optimization of combustion processes, and exhaust gas after-treatment led to a slight reduction of atmospheric CO levels. Renewed peaks in the CO time series n 2023 were caused by international transport of emissioms from large spread forest fires in North America.