Tools like genome sequencing and microalgal omics, including metabolomics, transcriptomics, and genomics, have led to an in-depth understanding of changes in cellular metabolism, interaction, and functions of different proteins leading to the production of high-value metabolites. The big data obtained through integrated omics with advanced techniques like confocal microscopy would enrich our understanding of the cellular dynamics in microalgae. The response of microalgae to N starvation and the corresponding changes happening in the proteome are very useful for the prediction of metabolic pathways, and knowledge is very crucial if we are to be able to stimulate desired fatty acid or triacylglycerol accumulation. Microfluorescence and electron microscopy are used to analyze the morphology and elemental composition of microalgae, whereas new techniques like confocal Raman microscopy, X-ray spectroscopy, secondary ion mass spectrometry and their combinations are explored to study microalgae. Data analysis using phylogeny and subcellular localization would help us determine key limiting factors in the functionality of metabolic pathways among microalgae.