Among the most important sections of the dzong that were completely reconstructed were the Machen Lhakhang where the sacred relics of Zhabdrung Ngawang Namgyal rest in thudam (permanent retreat), the Kuenrey (congregation hall), the Tsen Chhorten which houses the eight sandalwood chhortens, the Je Zimchung, and monks' living areas. Major restoration work was done on the Utse (central tower), the Kuenreys of the Drabi and Tshennyi divisions of the central monk body.
The entire environment around the dzong was given a facelift and the banks of the rivers secured against major floods in future.
The three-storey Machen Lhakhang was built out of cyprus wood with four entrance pillars intricately embossed with religious symbols in gold and silver. The inside of the lhakhang has been decorated with intrinsic and rich murals and frescos depicting the teachings of Lord Buddha.
The images of seven incarnations of the Zhabdrung were also installed in the lhakhang. An ornate 15-foot Kudung Chhorten was installed, made of sandalwood and encased in silver and gold and adorned with jewels like corals, pearls, turquoise, and other precious stones. It was constructed by 20 craftsmen over four years.
The Kuenrey, which was on the verge of collapse, was reconstructed on a grand scale. This great hall now features 12 30-foot cyprus pillars adorned in gilded brass plates embossed with elaborate religious sculpture.
In the Kuenrey sits the main 35-foot image of Buddha Shakyamuni, crafted out of a mixture of five menjim (precious substances) and medicinal clay.
The back wall carries images of the 16 arhats. The Buddha is flanked, on the right, by a 28-foot image of Guru Padmasambhava and, on his left, by a 28-foot image of Zhabdrung Ngawang Namgyal.
Along the left wall of the Kuenrey sit 48 three-foot images of the spiritual
masters of the kagyu lineage. On the right side are 48 three-foot
images of dongyu zinpa (lineage holders).
Under His Majesty's personal supervision, Bhutan's centuries-old building and artistic traditions came together and, over the past 12 years, thousands of carpenters and wood sculptors, metal and clay sculptors, masons, painters, fresco experts, electricians, blacksmiths, goldsmiths, silversmiths, tailors, and monk artisans re-lived history as they worked on the Punakha Dzong Renovation Project.