Abstract Single-cell multiomic analysis of the epigenome, transcriptome and proteome allows for comprehensive characterisation of the molecular circuitry that underpins cell identity, cell state, and cell type-specific gene regulatory networks. Technological advances, whereby multiple omics modalities can be simultaneously profiled in individual cells in a highly parallel manner, are already beginning to provide a step-change in our capacity to comprehend complex tissue biology during development and ageing, in health and disease, and upon treatment. However, the holistic interpretation of such datasets still presents a challenge due to an absence of approaches for the systematic joint analysis and evaluation of different modalities. Here, we present Panpipes, a set of computational workflows designed to automate the analysis of multimodal single-cell datasets by incorporating widely used Python-based tools to efficiently perform quality control, preprocessing, integration, clustering, and reference mapping at scale in the multiomic setting. Panpipes combines established and state-of-the-art methods to allow reliable and customisable analysis and evaluation of multiomic single-cell datasets, enabling users to investigate individual and integrated modalities, and to empower decision-making prior to downstream analyses and data interpretation.