This dataset concerns the fine lipid analysis of a lactic acid bacterium (Carnobacterium maltaromaticum CNCM I-3298) produced at its optimal activity. The dataset includes the chromatography analysis (TLC, HPLC, GC, SFC) of total lipids of C. maltaromaticum CNCM I-3298, the MS and NMR studies of the structures of neutral lipids, phospholipids and glycolipids of C. maltaromaticum CNCM I-3298 and the statistical analysis of the fatty acid composition of bacteria based on available data in the literature for the period from 1995 to 2022.