Abstract In recent years, the cultivation of algae has achieved attention of scientists and practicioniers due to the great variety of products that can be obtained, among which biofuels. The aim of this work is twofold. The first is to perform a profitability analysis of food and biofuel production from microalgae, in a small-scale setting. The second is to assess the economic impact of algae production systems on the dairy farms potentially interested in Southern Italy. The analysis was performed using financial and economic indicators and considering two system management scenarios, namely single and collective. Our results confirm that current microalgae production technology favors biofuel only as a co-product and that the production of high-value co-products improve profitability and net income in Southern Italian dairy farms, either in single or collective management. More specifically, the single management is more profitable, but the collective is more viable. The sensitivity analysis, based on the price uncertainty of algal biomass, confirms that the price of product is a critical parameter to ensure the investment feasibility in the agricultural context analyzed. Current study provides hints to entrepreneurs and managers operating in the agricultural sectors, interested in improving their firm’s performance through the adoption of a diversification strategy of business activities.