Pathognomonic accumulation of ubiquitin (Ub) conjugates in human neurodegenerative diseases such as Huntington’s disease has suggested the hypothesis that highly aggregated pathogenic proteins non-competitively interfere with 26S proteasome (26S) activity. We have explored possible mechanisms by which an N-terminal fragment of mutant huntingtin (N-htt) might inhibit 26S function. Exploiting a cell-free system using purified components we show that ubiquitinated N-htt -whether aggregated or not- does not choke or clog 26S. Quantitative flow-cytometry analysis shows that both Ub-dependent and Ub-independent proteasome reporters accumulate in cells when the cytoplasmic concentration of mutant N-htt exceeds a threshold above which its solubility can no longer be maintained, indicating that stabilization of 26S substrates is linked to N-htt aggregation and not to impaired function of Ub conjugation pathways. Single-cell time lapse image analysis shows that above its critical intracellular concentration, mutant N-htt becomes rapidly recruited to cytoplasmic inclusions that are initially devoid of Ub, and that UPS reporters accumulate, only in a small fraction of surviving cells, and only after a considerable lag . Although synthetically polyubiquitinated N-htt can compete with other Ub conjugates for access to 26S in vitro, quantitative mass spectrometry establishes that the vast majority of mutant N-htt in cells is not conjugated to Ub. Our data confirm that proteasomes are not directly impaired by aggregated N-terminal fragments of htt and instead suggest a model which links Ub accumulation to impaired function of the cellular proteostasis network.