Sea ice algae represent a key energy source for many organisms in polar food webs, but estimating their biomass at ecologically appropriate spatiotemporal scales remains a challenge. Attempts to extend ice-core derived biomass to broader scales using remote sensing approaches has largely focused on the use of under-ice spectral irradiance. Normalized difference index (NDI) based algorithms that relate the attenuation of irradiance by the snow-ice-algal ensemble at specific wavelengths to biomass have been used to explain up to 79% of the biomass of algae in limited areas. Application of these algorithms to datasets collected using tethered remotely operated vehicles (ROVs) has begun, generating methods for spatial sampling at scales and spatial resolution not achievable with ice-core sampling. Successful integration of radiometers with untethered autonomous underwater vehicles (AUVs) offers even greater capability to survey broader regions to explore the spatial heterogeneity of sea ice algal communities. This work describes the pilot use of an AUV fitted with a multispectral irradiance sensor to estimate ice-algal biomass along transects beneath land-fast sea ice (~2 m thick with minimal snow cover) in McMurdo Sound, Antarctica. The AUV obtained continuous, repeatable, multi-band irradiance data, suitable for NDI-type approaches, over transects of 500 m, with an instrument footprint of 4 m in diameter. Algorithms were developed using local measurements of ice algae biomass and spectral attenuation of sea ice and were able to explain 40% of biomass variability. Relatively poor performance of the algorithms in predicting biomass limited the confidence that could be placed in biomass estimates from AUV data. This was attributed to the larger footprint size of the optical sensors integrating small-scale biomass variability more effectively than the ice core in the platelet-dominated ice algal habitat. Our results support continued development of remote-sensing of sea ice algal biomass at m–km spatial scales using optical methods, but caution that footprint sizes of calibration data (e.g., coring) must be compatible with optical sensors used. AUVs offer autonomous survey techniques that could be applied to better understand the horizontal variability of sea ice algae from nearshore ice out to the marginal ice zone.