Abstract Motivation Modality matching in single-cell omics data analysis—i.e. matching cells across datasets collected using different types of genomic assays—has become an important problem, because unifying perspectives across different technologies holds the promise of yielding biological and clinical discoveries. However, single-cell dataset sizes can now reach hundreds of thousands to millions of cells, which remain out of reach for most multimodal computational methods. Results We propose LSMMD-MA, a large-scale Python implementation of the MMD-MA method for multimodal data integration. In LSMMD-MA, we reformulate the MMD-MA optimization problem using linear algebra and solve it with KeOps, a CUDA framework for symbolic matrix computation in Python. We show that LSMMD-MA scales to a million cells in each modality, two orders of magnitude greater than existing implementations. Availability and implementation LSMMD-MA is freely available at https://github.com/google-research/large_scale_mmdma and archived at https://doi.org/10.5281/zenodo.8076311.