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We present a combined microscopic and macroscopic study of YbxCo4Sb12 skutterudites for a range of nominal filling fractions, 0.15 < x < 0.75. The samples were synthesized using two different methods — a melt–quench–annealing route in evacuated quartz ampoules and a non-equilibrium ball-mill route — for which we directly compare the crystal structure and phase composition as well as the thermoelectric properties. Rietveld refinements of high-quality neutron powder diffraction data reveal about a 30–40% smaller Yb occupancy on the crystallographic 2a site than nominally expected for both synthesis routes. We observe a maximum filling fraction of at least 0.439(7) for a sample synthesized by the ball-mill routine, exceeding theoretical predictions of the filling fraction limit of 0.2–0.3. A single secondary phase of CoSb2 is observed in ball-mill-synthesized samples, while two secondary phases, CoSb2 and YbSb2, are detected for samples prepared by the ampoule route. A detrimental influence of the secondary phases on the thermoelectric properties is observed for secondary-phase fractions larger than 8 wt % regardless of the kind of secondary phase. The largest figure of merit of all samples with a ZT ∼ 1.0 at 723 K is observed for the sample with a refined Yb content of x2a = 0.159(3), synthesized by the ampoule route.