Field-based, rapid, and non-destructive techniques for assessing plant productivity are needed to accelerate the discovery of genotype-to-phenotype relationships in next-generation biomass grass crops. The use of hemispherical imaging and light attenuation modeling was evaluated against destructive harvest measures with respect to their ability to accurately capture phenotypic and genotypic relationships in a field-grown grass crop. Plant area index (PAI) estimated from below-canopy hemispherical images, as well as a suite of thirteen traits assessed by manual destructive harvests, were measured in a Setaria recombinant inbred line mapping population segregating for aboveground productivity and architecture. A significant correlation was observed between PAI and biomass production across the population at maturity (r2 = 0.60), as well as for select diverse genotypes sampled repeatedly over the growing season (r2 = 0.79). Twenty-seven quantitative trait loci (QTL) were detected for manually collected traits associated with biomass production. Of these, twenty-one were found in four clusters of co-localized QTL. Analysis of image-based estimates of PAI successfully identified all four QTL hotspots for biomass production. QTL for PAI had greater overlap with those detected for traits associated with biomass production than with those for plant architecture and biomass partitioning. Hemispherical imaging is an affordable and scalable method, which demonstrates how high-throughput phenotyping can identify QTL related to biomass production of field trials in place of destructive harvests that are labor, time, and material intensive.