Muhammed served as technical assistant and then as assistant archaeologist in the Department of History at Aligarh Muslim University. He was later selected as deputy superintendent archaeologist in Archaeological Survey of India. Muhammed was initially posted at Madras in 1988 and later transferred to Goa in 1991. In 1997, Muhammed was promoted as superintendent archaeologist and subsequently, served in Bihar, Uttar Pradesh, Chhattisgarh, Madhya Pradesh and Delhi. During this period, he also served as a tour guide to historic monuments for prominent foreign guests such as Pervez Musharraf and Barack Obama. In 2012, Muhammed Retired as regional director from Archaeological Survey of India.
Major archaeological discoveries
Excavated Ibadat Khana, the structure where Akbar proclaimed the formation of Composite religion known as Din-e Ilahi
KK Muhammed conserved the Barsoor and Samlur Temples in Dantewada District near Jagdalpur, Chhattisgarh. This area is known to be the seat of Naxal activities in the region. In 2003, KK Muhammed was able to convince Naxal activists and with their co-operation, conserved the Temples to its present-day state.
Bateshwar Complex restoration
is a complex of 200 ancient Shiva & Vishnu temples situated 40 kms away from Gwalior. These temples were built between 9th and 11th century during the Gurjara-Pratihara Dynasty, 200 years before Khajuraho. The area was under the control of Nirbhay Singh Gujjar and Gadariya Dacoits. KK Muhammed was successful in convincing the dacoits to let him restore these temples. He was able to restore 60 temples during his tenure. After the dacoits were eliminated by the police, the area was encroached by the mining mafia.
Facelift of Delhi's monuments
KK Muhammed was appointed as the Superintending Archaeologist of Delhi Circle, Archaeological Survey of India in 2008. His primary task was to carry out a major facelift activity at 46 monuments for the Commonwealth Games of 2010.
KK Muhammed conceived and executed the idea of building a Museum that contains the replicas of statues and stone carved sculptures across India. The museum, popularly known as the Replica Museum or the Children Museum is situated outside the Siri Fort Sports Complex, behind Siri Fort Auditorium in Delhi.
Autobiography
In 2016, KK Muhammad's Malayalam-language autobiography Njan Enna Bharatiyan was released. The book attracted controversy due to his claim that the Marxist historians sided with the extremist Muslim groups and derailed attempts to find an amicable solution to the Ayodhya dispute. According to him, archaeological excavations at Ayodhya clearly indicated the presence of a temple below the mosque, but the leftist historians dismissed these, and even tried to mislead the Allahabad High Court.