Recent research suggests that micronutrients such as Mn may limit growth of slow-growing biological soil crusts (BSCs) of the Colorado Plateau (USA). BSCs contribute strongly to arid ecosystem function and are easily degraded, creating a need for new restoration tools. The possibility that Mn fertilization could be used as a restoration tool for BSCs has not been tested previously. Using greenhouse microcosms containing the BSC lichen, Collema tenax, and early successional, cyanobacterially-dominated BSC transplants in the field, we investigated the hypothesis that Mn limits photosynthesis and consequently growth of BSCs. The greenhouse experiment provides scant evidence to support our hypothesis; furthermore, we found that other nutrients (P, K, and Mg) increased the production of scytonemin, an important sunscreen pigment, but only when not added with Mn (P = 0.01). We propose three alternative hypotheses for this pattern: 1) Mn suppresses scytonemin production, 2) Mn suppresses scytonemin production at low light, when it is an unnecessary photosynthate sink, and 3) Mn is involved in osmoregulation, and scytonemin synthesis indicates osmotic stress. In the field experiment, BSC communities subjected to five different fertilizer treatments have not yet diverged, although the rate of succession is fastest in BSCs receiving Mn only, and is nearly 2× faster than BSCs receiving Zn only (P = 0.03). Contrary to the greenhouse results, the pigment scytonemin was unresponsive (P = 0.59). Although the effect of Mn fertilization on photosynthesis or growth of BSCs is inconclusive, the role of Mn in stress tolerance mechanisms should be investigated further.