The temple has a simple construction with the original shrines of Ganapathy and Subramanian (along with the Navagrahas) housed inside two concrete structures located side by side facing west. Between these two structures is located the stairs leading to the more recent elevated structure which houses the shrines of several other Gods and Goddesses. These new shrines were added in the year 2000 and include those for Shiva, Parvathi, Rama, Dakshinamurthi and Chandikeshwara. The entire building covers an area of just around 5,000 square feet (460 m2), and there are no outer walls. There is a Peepal tree in front of the Ganapathy shrine.
The temple complex includes a ground behind the building. The busy Eloor-Kalamassery road runs just in front of the temple. The space from the temple's front and the road is so short (around 30 feet) that it has earned the deity the dubious nickname of 'Road-side Ganapathy'.
The devotees refer to elephants as Lord Ganesh's incarnation. It has been the regular annual practice at the Mahaganapathy temple for the last 20 years to conduct a large-scale Ashta Dravya Maha Ganapathy Havana and Aanayoottu on the first day of the Karkkidakom month of the malayalam calendar. Gajapooja also is conducted once every four years.