Responsible for cellular energy production, mitochondria contain a semi-independent genome (mtDNA), which has undergone intense reorganization leading to peculiar transcriptional and post-transcriptional mechanisms. In this study dRNAseq-based mitochondrial transcriptome analysis was performed on Nicotiana tabacum and focused on end processing, one of the necessary processing steps for correct translation. Naturally occurring primary (TSS) and processed (PS) ends were discriminated and candidates were verified by RACE-PCR. Treatments were chosen to investigate the effect of light exposure and spectinomycin was used to reduce the impact of plastidial factors. Both the 5 and 3 termini of major mitochondrial genes were identified and correspondent involved processing events were proposed. According to previous studies, high variability of processed 5 ends was found while 3 ends, which mainly result from stable structure formation, are generally conserved. The occurrence of seven ncRNAs was also confirmed. Promoter analysis performed on dRNAseq-based listed TSSs failed in the identification of conserved motifs, similar to the scenario depicted in Arabidopsis, suggesting a general peculiarity of dicot mitochondria. Based on previously published criteria, oTSS is the most represented class in tobacco mtDNA, supporting the occurrence of intergenic transcription and relaxed control in transcription initiation: TSSs are found scattered along the whole genome and suggested to be functional although at relatively low level. Based on the extension of detected transcription by dRNAseq data, the length of trans-spliced introns and operon organization of tobacco mitochondrial genes were suggested: remarkably, the majority of annotated non-coding ORFs showed relatively high transcription level. Quantitative analysis identified the occurrence of the precursors and the mature transcript of nad5d and of two potential ncRNAs and the order of the processing events has been proposed.