The inlet manifold is outside the cylinder. With the engine not running then pressure, both in the manifold & the cylinder, is equalised with ambient.
When the engine is running it 'sucks' air or air/fuel mixture out of the inlet manifold, past the inlet valve & into the cylinder. Then the inlet valve closes & the mixture that is now in the cylinder is compressed, not the air or air/fuel mix that remains in the inlet manifold.
Meanwhile replacement air or air/fuel is trying to equalise the (now reduced) pressure in the manifold - except that the cycle is repeated.
The air has inertia & cannot move to refill the volume instantaneously so the overall effect of the engine sucking air out of the manifold whilst at the other end air is trying to refill the manifold, is a reduction in manifold pressure.
All the above for a normally aspirated engine of course.
Hope this helps.