<p>We report measurements of electron spin echo envelope modulation (ESEEM) performed at millikelvin temperatures in a custom-built high-sensitivity spectrometer based on superconducting micro-resonators. The high quality factor and small mode volume (down to 0.2 pL) of the resonator allow to probe a small number of spins, down to 5 ⋅ 10<sup>2</sup>. We measure 2-pulse ESEEM on two systems: erbium ions coupled to <sup>183</sup>W nuclei in a natural-abundance CaWO<sub>4</sub> crystal, and bismuth donors coupled to residual <sup>29</sup>Si nuclei in a silicon substrate that was isotopically enriched in the <sup>28</sup>Si isotope. We also measure 3- and 5-pulse ESEEM for the bismuth donors in silicon. Quantitative agreement is obtained for both the hyperfine coupling strength of proximal nuclei, and the nuclear spin concentration.</p>