Due to the inherent toxicity of protein aggregates, the propensity of natural, functional amyloidogenic proteins to aggregate must be tightly controlled to avoid negative consequences on cellular viability. The importance of controlled aggregation in biological processes is illustrated by spidroins, which are functional amyloidogenic proteins that form the basis for spider silk. Premature aggregation of spidroins is prevented by the N-terminal NT domain. Here we explored the potential of the engineered, spidroin-based NT domain in preventing protein aggregation in the intracellular environment of human cells. We show that the NT domain increases the soluble pool of a reporter protein carrying a ligand-regulatable aggregation domain. Interestingly, the NT domain prevents the formation of aggregates independent of its position in the aggregation-prone protein. The ability of the NT domain to inhibit ligand-regulated aggregation was evident both in the cytosolic and nuclear compartments, which are both highly relevant for human disorders linked to non-physiological protein aggregation. We conclude that the spidroin-derived NT domain has a generic anti-aggregation activity, independent of position or subcellular location, that is also active in human cells and propose that the NT domain can potentially be exploited in controlling protein aggregation of disease-associated proteins.