MetaFlux is a global, long-term carbon flux dataset of gross primary production and ecosystem respiration that is generated using meta-learning. The principle of meta-learning stems from the need to solve the problem of learning in the face of sparse data availability. Data sparsity is a prevalent challenge in climate and ecology science. For instance, in-situ observations tend to be spatially and temporally sparse. This issue can arise from sensor malfunctions, limited sensor locations, or non-ideal climate conditions such as persistent cloud cover. The lack of high-quality continuous data can make it difficult to understand many climate processes that are otherwise critical. The machine-learning community has attempted to tackle this problem by developing several learning approaches, including meta-learning that learns how to learn broad features across tasks to better infer other poorly sampled ones. In this work, we applied meta-learning to solve the problem of upscaling continuous carbon fluxes from sparse observations. Data scarcity in carbon flux applications is particularly problematic in the tropics and semi-arid regions, where only around 8–11% of long-term eddy covariance stations are currently operational. Unfortunately, these regions are important in modulating the global carbon cycle and its interannual variability. In general, we find that meta-trained machine models, including multi-layer perceptrons (MLP), long-short-term memory (LSTM), and bi-directional LSTM (BiLSTM), have lower validation errors on flux estimates by 9–16% when compared to their non-meta-trained counterparts. In addition, meta-trained models are more robust to extreme conditions, with 4–24% lower overall errors. Finally, we use an ensemble of meta-trained deep networks to generate a global product of ecosystem-scale photosynthesis and respiration fluxes from in-situ observations to daily and monthly global products at a 0.25-degree spatial resolution from 2001 to 2023, called "MetaFlux". We also checked for the seasonality, interannual variability, and correlation to solar-induced fluorescence of the upscaled product and found that MetaFlux outperformed state-of-the-art machine learning upscaling models, especially in critical semi-arid and tropical regions.