Lund Human Mesencephalic (LUHMES) cells are a cellular model of Parkinson’s disease (PD) that can be grown as undifferentiated cells and be differentiated into dopaminergic neurons. Here we have identified a series of changes in mitochondrial phenotypes that occur throughout the differentiation process and need to be considered when using this model in a PD context. Besides the acquisition of a neuronal dopaminergic phenotype with increased levels of tyrosine hydroxylase, dopamine receptor D2 or β-III-tubulin, we identified changes in mitochondrial markers reflecting an important reduction in mitochondrial mass during differentiation, alongside a decrease in Complex I linked respiration but not in Complex I and II linked respiration. In addition, we have investigated the possibility that enhancing mitochondrial quality control via activation of the caseinolytic peptidase (CLPP) may have a neuroprotective effect in this model in the context of a PD-relevant challenge. To this end, we have observed that CLPP activation induces an increase in mitophagy and partially rescues neuronal cell death induced by α-synuclein pre-formed fibrils. However, the neuroprotective effect was dependent on the type of CLPP activator employed, and its binding and activation properties. Gene expression changes induced by CLPP activation analysed by RNA sequencing also indicate that distinct signalling pathways are activated depending on the type of activator employed, and they may determine the cellular decision to survive or die.