The discovery and deployment of earth-abundant electrocatalysts for hydrogen evolution is central to the use of molecular hydrogen as a viable fuel. The edges of molybdenum sulfide are able to mediate proton adsorption and dihydrogen formation at relatively low overpotentials in acidic media. From a practical perspective, an optimal electrocatalyst must combine electrode level efficiency (reflected by high current densities and low Tafel slopes and overpotentials) with high intrinsic catalytic activity (measured by turnover frequency). Herein, we map both sets of parameters for molybdenum sulfide catalysts as a function of the annealing temperature across their amorphous to crystalline phase transition. Studies of local structure indicate that with increasing annealing temperature, molecular precursors are initially cross-linked to form [Mo3S13]2− clusters characterized by both apical/bridging S22− and unsaturated/terminal S22− moieties, which in turn are consumed to nucleate ultra-thin crystalline MoS2 domains. With increase of the annealing temperature, these nuclei coalesce to form larger nanosheets. Annealing and the resulting amorphous to crystalline transition involves a trade-off between the number of available sites (which is decreased with increasing crystallite size) and the intrinsic activity of the sites (which is improved with increasing crystallinity). Optimal hydrogen evolution reaction (HER) activity is observed for the molybdenum sulfide sample prepared by annealing at 300 °C, which comprises ultra-thin MoS2 nuclei embedded within a matrix of [Mo3S13]2− clusters. This sample is characterized by an overpotential value η10 of 176 mV, a Tafel slope of 49.2 mV dec−1, a turnover frequency of 1.15H2 per s per active site at −0.2 V versus reversible hydrogen electrode (RHE), and furthermore exhibits reasonable stability upon prolonged electrochemical cycling. The amorphous samples are found to be more susceptible to oxidation, which degrades the stability of the catalysts. The mapping of electrode-level parameters and intrinsic activity as a function of crystallite size provides vital design principles for constructing a viable electrocatalyst.