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In this work, we report a mathematical framework which predicts the degree of alignment (DoA) in an in-situaligned additively manufactured 3D printed bonded magnets. A multiphysics model is developed which couples the harmonious interactions of magnetic particles in a viscous flowing polymer under the presence of an external magnetic field. The hydrodynamic fluid-particle interaction is paired with the magnetophoretic force to predict the particle trajectory and distribution during extrusion through a 3D printer nozzle. Succeeding the force balance, a magnetohydrodynamic torque equilibrium analysis is performed to predict the net-orientation of the magnetic particles as a function of the applied field strength, viscous forces, and particle-to-particle interactions (P2P). Experimental validation of the DoA predictions is performed using 65 vol.% Nd-Fe-B+Sm-Fe-N in Nylon12 (DoAexp= 0.620 and DoAtheory= 0.686) and 15 vol.% Sm-Co in PLA (DoAexp= 0.830 and DoAtheory= 0.863). A parametric analysis is performed to analyze the effect of operating and design parameters like alignment field strength, magnetic loading fraction, extrusion load, and particle size. The model predicts a competing behavior between particle-fluid and particle-particle interactions under the presence of an applied field. The model provides a framework to efficiently predict the DoA in tandem with a functionalized-magnetic 3D printer and allows the user to adjust the operating parameters according to the desired DoA.