Yes, in vivo studies present more realistic results since the phytoconsituents are interacting directly with the system/model. Some plants show striking in vitro antimicrobial activities only to lose that activity in vivo. Nevertheless in vitro studies are still relevant as they can provide relevant pointers. First you will need to carry out the antimicrobial assay using your crude extracts on the pathogens and get parameters like antimicrobial sensitivity, diameter of zone of inhibition, minimum bactericidal concentration and minimum inhibitory concentration. This can now tell you whether to continue with the in vivo tests.
The in vitro studies just give you a key criteria to know MIC and MBC of any natural substances and kind of microorganisms that are inhibited by the natural agent. In vivo is completely different conditions where many factors can interfere action of the antimicrobial agent such as body fluids and probiotics. Of course in vivo is the intended applications and any success in any in vivo experiment is nice .Recently you shuld work with an identified bioactive substance not with the whole plant extract