Microalgae have been identified to produce a plethora of bioactive compounds exerting growth stimulating effects on plants. The objective of this study was to investigate the plant-growth-promoting effects of three selected strains of eukaryotic green microalgae. The biostimulatory effects of two Chlorella species (MACC-360 and MACC-38) and a Chlamydomonas reinhardtii strain (cc124) were investigated in a Medicago truncatula model plant grown under controlled greenhouse conditions. The physiological responses of the M. truncatula A17 ecotype to algal biomass addition were characterized thoroughly. The plants were cultivated in pots containing a mixture of vermiculite and soil (1:3) layered with clay at the bottom. The application of live algae cells using the soil drench method significantly increased the plants’ shoot length, leaf size, fresh weight, number of flowers and pigment content. For most of the parameters analyzed, the effects of treatment proved to be specific for the applied algae strains. Overall, Chlorella application led to more robust plants with increased fresh biomass, bigger leaves and more flowers/pods compared to the control and Chlamydomonas-treated samples receiving identical total nutrients.