In lupus, Toll-like receptor 7 (TLR7) and TLR9 mediate loss of tolerance to RNA and DNA, respectively. Yet, TLR7 promotes disease, while TLR9 protects from disease, implying differences in signaling. To dissect this ‘TLR paradox’, we generated two TLR9 point mutants (lacking either ligand (TLR9^K51E) or MyD88 (TLR9^P915H) binding) in lupus-prone MRL/lpr mice. Ameliorated disease of Tlr9^K51E mice compared to Tlr9^−/− controls revealed a TLR9 ‘scaffold’ protective function that is ligand and MyD88 independent. Unexpectedly, Tlr9^P915H mice were more protected than both Tlr9^K51E and Tlr9^WT mice, suggesting that TLR9 also possesses ligand-dependent, but MyD88-independent, regulatory signaling and MyD88-mediated proinflammatory signaling. Triple-mixed bone marrow chimeras showed that TLR9–MyD88-independent regulatory roles were B cell intrinsic and restrained differentiation into pathogenic age-associated B cells and plasmablasts. These studies reveal MyD88-independent regulatory roles of TLR9, shedding light on the biology of endosomal TLRs.