ABSTRACT We present a new class of estimators for computing small-scale power spectra and bispectra in configuration space via weighted pair and triple counts, with no explicit use of Fourier transforms. Particle counts are truncated at $R_0\sim 100\, h^{-1}\, \mathrm{Mpc}$ via a continuous window function, which has negligible effect on the measured power spectrum multipoles at small scales. This gives a power spectrum algorithm with complexity $\mathcal {O}(NnR_0^3)$ (or $\mathcal {O}(Nn^2R_0^6)$ for the bispectrum), measuring N galaxies with number density n. Our estimators are corrected for the survey geometry and have neither self-count contributions nor discretization artefacts, making them ideal for high-k analysis. Unlike conventional Fourier-transform-based approaches, our algorithm becomes more efficient on small scales (since a smaller R0 may be used), thus we may efficiently estimate spectra across k-space by coupling this method with standard techniques. We demonstrate the utility of the publicly available power spectrum algorithm by applying it to BOSS DR12 simulations to compute the high-k power spectrum and its covariance. In addition, we derive a theoretical rescaled-Gaussian covariance matrix, which incorporates the survey geometry and is found to be in good agreement with that from mocks. Computing configuration- and Fourier-space statistics in the same manner allows us to consider joint analyses, which can place stronger bounds on cosmological parameters; to this end we also discuss the cross-covariance between the two-point correlation function and the small-scale power spectrum.