Microencapsulation procedures have recently focused attention on designing novel microspheres via green synthesis strategies. The use of chitosan (CS) as an encapsulating material has increased interest due to its unique bioactive properties and the various crosslinking possibilities offered by their functional groups. The consolidation of the microspheres by physical crosslinking using sodium tripolyphosphate (TPP) combined with chemical crosslinking using vanillin (VA) open new opportunities in the framework of green dual crosslinking strategies. The developed strategy, a straightforward technique based on an aqueous medium avoiding complex separation/washing steps, offers advantages over the processes based on VA, mostly using water-in-oil emulsion approaches. Thus, in this work, the combination of TPP crosslinking (3, 5, and 10 wt.%) via spray-coagulation technique with two VA crosslinking methods (in situ and post-treatment using 1 wt.% VA) were employed in the preparation of microspheres. The microspheres were characterized concerning morphology, particle size, physicochemical properties, thermal stability, and swelling behavior. Results revealed that the combination of 5 wt.% TPP with in situ VA crosslinking led to microspheres with promising properties, being an attractive alternative for natural bioactives encapsulation due to the green connotations associated with the process.