With objective to design cyanobacterial biorefinery, taking Lyngbya as a model organism, a detail sequential protocol has been developed for production of UV protectant and lipids. This study addresses ultra violet radiations (UVR), exposure time of UVRT, nitrogen stress, salinity, oxidative stress to produce UV protectant and lipid in cyanobacteria. To evaluate these parameters a design of experiment (DOE; using a 2 k design) was performed. Based on chemical solubility property of UV protectant in form of mycosporine like amino acid (MAAs) and lipids were extracted. Quantitative and qualitative assay of UV protectant was confirmed by spectrophotometric scanning and Fourier-transform infrared spectroscopy and lipid through fatty acid methyl esters analysis. Nitrogen abundance and high oxidative stress is helpful in the synthesis of UV protectant. This study concluded, UV exposure is good strategy to induce synthesis of UV protectant and saturated lipid productivity. This biorefinery approach encourages economical and environmentally sustainable options.