We use 6 yrs of accurate hyperfine frequency comparison data of the dual rubidium and caesium cold atom fountain FO2 at LNE-SYRTE to search for a massive scalar dark matter candidate. Such a scalar field can induce harmonic variations of the fine structure constant, of the mass of fermions, and of the quantum chromodynamic mass scale, which will directly impact the rubidium/caesium hyperfine transition frequency ratio. We find no signal consistent with a scalar dark matter candidate but provide improved constraints on the coupling of the putative scalar field to standard matter. Our limits are complementary to previous results that were only sensitive to the fine structure constant and improve them by more than an order of magnitude when only a coupling to electromagnetism is assumed.