Despite advances in single-cell multi-omics, a single stem or progenitor cell can only be tested once. We developed clonal multi-omics, in which daughters of a clone act as surrogates of the founder, thereby allowing multiple independent assays per clone. With SIS-seq, clonal siblings in parallel “sister” assays are examined either for gene expression by RNA sequencing (RNA-seq) or for fate in culture. We identified, and then validated using CRISPR, genes that controlled fate bias for different dendritic cell (DC) subtypes. This included Bcor as a suppressor of plasmacytoid DC (pDC) and conventional DC type 2 (cDC2) numbers during Flt3 ligand-mediated emergency DC development. We then developed SIS-skew to examine development of wild-type and Bcor-deficient siblings of the same clone in parallel. We found Bcor restricted clonal expansion, especially for cDC2s, and suppressed clonal fate potential, especially for pDCs. Therefore, SIS-seq and SIS-skew can reveal the molecular and cellular mechanisms governing clonal fate. Display omitted •Clonal multi-omics assesses daughters from one founder cell for different features•SIS-seq identifies the genes that control clonal fate•SIS-skew identifies how perturbation affects clonal fate•Bcor is identified as a novel regulator of dendritic cell subset development In the absence of a time machine, a single cell cannot be tested more than once in a destructive assay. Tian et al. instead develop clonal multi-omics to bypass this challenge and identify Bcor as a regulator of dendritic cell fate.