Mnajdra lies about 1 km (0.6 miles) downhill from Hagar Qim, on a low elevation overlooking the sea and the tiny islet of Filfla. Mnajdra is assigned to the Ggantija phase (before 3000 BC) by some guidebooks, but according to Bonanno, both complexes were built during the Tarxien phase (3000 BC - 2500 BC). In any case, the sites are not considered to be contemporaneous, and the relationship between them is not known with any degree of certainty.
The cloverleaf plan of Mnajdra appears more regular than that of Hagar Qim, and seems reminiscent of the earlier complex at Ggantija. The south, or lower, temple is said to be aligned with the solar equinoxes. This alignment may be accidental. If not, it is the only such alignment which has been observed so far in the temples.
Important and pleasing features of Mnajdra include elaborate pitted decoration, well-constructed stone altars and niches, and fine corbelling and wallwork.