The current need to reduce greenhouse gas emissions is pushing the incorporation of technologies to achieve industrial decarbonisation in Europe. The present work develops a techno-economic tool that analyses different scenarios to assess microalgae production in some foreseeable situations, and determines the ones in which the contribution of CO2 biofixation would be relevant. The biomass production cost ranged between 0.41 and 13.06 €/kg. It was also possible to recover 0.03–0.1 €/kg CO2 depending on its temporal variation and the amount of biomass produced. This analysis aims to identify the technologies and operational conditions viable for the different applications. According to the scenarios considered, microalgae technology could be competitive if the emission rights market reaches expected costs of approximately 50 €/t CO2 in the near future (2030). Otherwise, microalgae related processes can be also reliable for different medium- and high-value applications, but only if adequate technologies and operational conditions are considered. The information here provided supports decision making processes for microalgae based processes.