Lipid microparticles (LMP) made with anhydrous milk fat (AMF) and fully hydrogenated soybean oil (FHSBO) may provide crystallization and control the polymorphic stability of lipid matrices. The present study investigated the production of LMP and their stability during 120 days of storage at 5, 10, and 25 °C. LMP were produced using lipid blends 90:10 and 80:20 (AMF:FHSBO % w/w) sprayed in a double fluid atomizer at 1 bar, in a chilled chamber (1 ± 1 °C), and analyzed once a week for particle size, morphology, melting behavior, and polymorphic habit. LMP presented a spherical shape and a volumetric diameter of 10 μm. Both LMP presented melting behavior within a wide temperature range. The polymorphic habit was affected by the lipid base and the storage temperature. LMP stored at 25 °C tended to exhibit a more stable polymorphic form. An increase in FHSBO concentration led to an increase in stability, exhibiting the β form, with no polymorphic changes after 14 or 21 days, remaining stable up to 120 days, for all microparticles. Our results suggested the potential of LMP for several technological applications such as crystallization inducer, structuring agent, and as wall material, due to their thermal and polymorphic stability.