MicroRNAs (miRNAs) are small non-coding RNAs which modulate gene expression, promoting the degradation of target mRNAs or altering their translation. In the last decade, the role of miRNAs has been largely investigated, providing interesting evidence about the key role of these molecules in plant cell and molecular biology. Recently, our research team has sequenced the miRNome of Moringa oleifera Lam., a plant species widely used in African ethnobotanical traditions, including food practices and folk medicine. In addition, in the last years, our group has also evaluated the differences between the miRNomes from the M. oleifera leaf and leaf-derived callus, respectively. The present communication reports the study of the miRNA expression profile in M. oleifera young plants grown in vitro under different conditions. In particular, seedlings/young plants cultivated for 2, 15, 30, and 60 days or grown for 30 days and subjected for other 30 days to biotic (i.e., chemical inducer of systemic acquired resistance) and abiotic (i.e., darkness, cold) stressors were analyzed. After nucleic acid extraction and retrotranscription, the level of 19 specific miRNAs was evaluated by qPCR assay. Overall, the amount of all miRNAs was higher in 2-day-old seedlings than in older ones. Cold and biotic stimuli induced the overexpression of more than half of the miRNA set, while darkness triggered downregulation or stabilization of most examined miRNAs. In order to clarify the molecular networks and signalling pathways potentially modulated by moringa miRNAs, the putative mRNA targets of the selected miRNAs were predicted using the psRNATarget bioinformatics approach. This study presents novel and interesting information about the role of specific miRNAs in M. oleifera seedlings during their initial developmental stages, as well as in the presence of simulated environmental stresses.