In order to maximize the economic return from microalgae production, the feasibility of thermochemically converting microalgae by-products which have had one or more biochemical components extracted (lipids and/or protein) needs to be considered. The extracted microalgae are waste stemming from microalgae biorefineries where biodiesel and/or valuable proteins/peptides have been produced. The biorefinery scheme of maximized microalgae utilization based on isolation of lipids or lipids and proteins combined, and the thermochemical conversion of the remaining fractions are discussed in this study. The biopolymer components of Nannochloropsis gaditana were extracted to form a lipid fraction, a protein fraction and a carbohydrate-rich residue. The lipid extraction efficiency reached 76.9 wt.%, however, the efficiency of protein extraction was 42.2 wt.% due to the inability of the extraction process to remove all protein. The surface functional groups and thermochemical characteristics of extracted components were investigated by FTIR and py-GC/MS, respectively. The FTIR results suggested that the extraction process disrupted the microalgae cell walls and released intracellular components. Lipids are recommended to be extracted for biofuel production by transesterification. For specific high protein-containing microalgae, protein extraction has to be considered to obtain high value proteins and derived chemicals. After the extraction of high value products, the carbohydrate-rich residue which is considered of low value, can be used as a fast pyrolysis feedstock instead of the whole microalgae. The pyrolysis chemical pathways as a function of temperature were schematized in order to better understand the reaction mechanisms in microalgae pyrolysis. The formation of alkanes and alkenes at higher temperatures were stemming from the long-chain alcohols and carboxylic acids. The formation pathways of N-heterocyclic compounds include Maillard reactions, cracking of amino acids and the cyclization of amines and amides.