With the beginning of the reign of Murshid Quli Khan II, the disinterest so far shown to Jagannath worship underwent a different turn. Mir Habib, a right hand man of Murshid Quli II, took particular interest in taking measures for the reinstatement of the idol of Jagannath in the temple at Puri.  This friendly and generous attitude of Murshid Quli to the Raja of Khurda and Jagannath was considered as a big relief to the Hindus of Orissa.
Thus in the Mughal period, except during the reign of Akbar and Murshid Quli II, the worship at the temple of Jagannath was very often disturbed. Nothing was done to allay the suspicion and fear of the priestly class, the Superintendent of the temple and the devotees of Jagannath that they were free to worship Jagannath without any interference. On the other hand, occasionally some governors or generals in fact raided or desecrated the temple, which made their probable fear a fact or reality.
Again the frequent attacks on the Raja of Khurda made the worship of Jagannath some times either unpracticable or difficult. The treatment shown to Jagannath and the Superintendent of the temple by most of the Muslim rulers or officers must have given the impression that in general, the Muslims had no regard for the religious susceptibility of the other people.
In the Muslim period, a pilgrim tax on the pilgrims, coming from various parts of India to visit the temple of Jagannath was imposed in Orissa. But it is not definitely known when and who introduced it. It is just possible that this pilgrim tax might have been introduced during the rule of Aurangzeb.
One may infer that the Muslim officers might be collecting tax at those principal ghats at Atharanala and Lokanath leading to the town, and Jagannath from the north and south respectively, as was done in later period by the Marathas at the end of the Mughal rule. The amount of pilgrim tax collected from the pilgrims to Orissa under every Muslim ruler is not known. But during the administration of Raqi Khan, Muslim government was deprived of revenue amounting to 9 lakhs of rupees a year collected from pilgrim tax. This shows that the income from the pilgrim tax was usually at least not less than 9 laks of rupees per year.  But as it appears during the Mughal rule, most of the time the idol was taken away from Puri to a place of safety and there was disturbance in worship, and all the tax gathering Mughal generals except Murshid Quli II cared little for income under this head.
Islam and its prosperity in Orissa
Muslim migration to Orissa was continuous after its conquest and Muslims settled in the new province with a new religion and culture. Along with the administrators, generals, traders and camp followers came in train, ulemas and saints to cater to their religious needs.
Under the patronization of Muslim governing and religious-minded people, the Muslim religious institutions flourished. First Cuttack, the Muslim capital of Orissa, grew to be the most important place of Muslim religious institutions, and later on with the penetration of the Muslim population to the interior of the province, the Muslim mosques and tomb of saints were found in other parts of the province.
Ekram Khan constructed a mosque in Balubazar, in Cuttack and dedicated it to Shahajada Begum (Zebbunisa), daughter of Aurangzeb.  Shuja-uddin built the famous Qadam Rasul mosque at Cuttack.  Some of the other principal monuments which were erected during the Muslim period at Cuttack were Diwan-bajar masjid, Ujale Khan masjid of Mahamadia Bazar and a masjid inside the compound of Lalbag. The religious-minded Muslim governors, Deputy governors or some officers certainly encouraged the growth of Muslim institutions by their generous grants. Probably the more important role was played by the Muslim saints who could spread Islamic ideas and left reputation behind them. This is testified from the tombs of saints, like those of Shah Mansur and Panja Shah at Oriya Bazar and Bakshi Shahib in Barabati fort, Cuttack, which have been practically places of adoration and pilgrimage to all those Muslim devotees.
The other two saints who were famous during the Muslim rule were Malang Shah and Mastan Shah, and their tombs are found in the compound of the Cuttack branch of G.P.O. and on cantonment road respectively. All these saints were well-known for their piety, kindness, pious and exemplary life they led. They were respected and loved by the Hindus and Muslims. 
With the spread of Muslim power to other parts of Orissa, Muslim monuments were built there. The Qadam Rasul built at Balasore by the Taqi Khan and Abu Nasar mosque were built there. The Qadam Rasul built at Balasore by Taqi Khan and the Abu Nasar mosque built at Jajpur are indicative of the prosperity of Islam at places other than Cuttack proper.
A dargha known as Takht-I-Sulaiman was constructed during the reign of Nawab Shuja-uddin Muhammad Khan in honour of a holy saint who came to the mountain top of Alti in mauza Charnangal in the present Cuttack district.  The tombs of saints at Pipli like the tomb of Sayyid Sultan, Sindhy Bakhs saheb and the tomb of Bokhari saheb at Kaipadar a tomb of Sayyid Bokhari at Jajpur  remind one of how the saints moved from one part of Orissa to the other.
Orissa was a place where not only Sunni scholars, saints and learned men were available but also Shia scholars and saints too. Shah Mansur was a Shia saint. His tomb lies inside Lalbag. It is visited by both Muslims and Hindus. Shia scholars were envied by the Sunni saints. This shows the animosity that was prevalent during the Muslim period, more particularly during the rule of Aurangzeb. 
There was a noted saint in Orissa called Shah Qasim Ho Allahi. He claimed to have supernatural power. He was a Sunni saint and all that he did was to convert the Shias of Orissa into Sunni faith not by force but by magic and miraculous deeds. He succeeded in persuading one Hakim Tahir, a Shia to renounce Shiaism and to be his disciple. 
Orissa attracted some reputed Muslim scholars. For example, Mirza Zarif stayed in Orissa for three years. He was well-versed in jurisprudence and natural science. He was the maternal uncle of Be-dil, who came from Bihar for his visit to Orissa. Mirza Zarif cured Sayyid Muhammad from swollen limb. Sayyid Muhammad was nobody but Khan-i-Dauran, the governor of Orissa. There were also many dervishes in Orissa who were having high knowledge in spiritual matters. 
The Muslim government granted a good deal of lands to the poor, destitutes, holy men, ulemas, maulavis, saints and to the different Muslim religious institutions for their maintenance. Ten batis of land were granted by the Mughal government to the holy men like Abdul Hamid and others for their maintenance and for praying to God for the longevity of the throne. In the year 1686, the Nawab of Bengal and Orissa granted 5 batis of land to Masabat Aisa Bibi of Jajpur for her maintenance. Aurangzeb in the year 1704-5 gave a grant of 2 batis of land to Shaikh Abdus Salam for his maintenance. [ ]
It is wrong to say that the generosity of the Muslim government was extended only to patronize the Muslim monuments, Muslim saints and Muslim religious-minded persons. Consistent with the tradition maintained by the previous government and having same regard to the established Hindu institutions, the Muslim government was found to confirm the lands already enjoyed by the Hindu gods or to grant new lands for the Hindu religious purposes, with a view to winning the popularity of the Hindus. For example, once Alivardi Khan granted one bati of land to Sham Mohapatra in Usuna village in Kadinda Parana for the purpose of khairat.
Sometimes eminent Muhammadan noble men or provincial governors granted certain lands to the Hindus or Hindu institutions as charity. It is stated once some Guljari Husain granted the entire mauza of Baghua to Shri Jagannath Thakur (God) through Mohan Das for amrit-manohi.
Again Shuja-uddin Muhammad Khan granted one bati and two manas of land to Purusottam Bharati in Suasahi village for the maintenance of sadabart. To add to this, it may be stated that Raja Sarf-uddin Husain granted the entire village of Jagannathpur to adhibari Gopinath Das for the expenses of travelers and beggars. Choudhury Fateh Khan and others granted 7 batis 7 manas and 15 gunthas of land to Radhakanta Thakur through Balki Das in Kandarpur as khairate in 1748.
 Ibid. p. 77.
 The amount accruing from pilgrim tax in Mughal period is considerably higher than the amount of rupees from 2-1/2 lakhs to 5 lakhs collected at the early British rule in Orissa. (26 September 1803, Melville to Govt., Bengal Secret and Political Consultations, 1st March 1804, No. 16). It seems that the amount collected by the Mughals might have included a religious tax under the head of Sayar, which was also collected by the Marathas, or the rate of Mughal pilgrim tax must have been higher than that realized by the Marathas or British. The Marathas were collecting 3 lakhs of rupees per year. (Orme MSS India, Vol. 18, p. 16).
 O.H.R.J., Vol. VI, No. 4, pp. 285-286. Also vide Early European Travellers in Nagput Territories, p. 55.
 Banerjee, R.D., Vol. II, p. 88.
[4a] O.H.R.J., Vol. VI, No. 4., p. 290.
 Asad was a Shia who was thrown down from his palanquin by a lightening bolt and could not be cured. Chahar-Unsur, p. 70ff; Hakim Tahir and Narudin Tahir were also Shias.
 Copy of a letter No. 5532/E dated 14 Aug. 1950 from the Under Secretary to government of Orissa to District Magistrate Cuttack.
 Stirling, p. 113.
 Chahar-Unsur, p. 70ff (OPL No. 0891 551030 Bed, Accession No. 1800 Patna).
 Chahar-Unsur, p. 70ff
From "Orissan Under the Mughals: From Akbar to Alivardi, a fascinating Study of the Socio Economic and Cultural History from Orissa" by B.C. Ray, M.A. Ph.D (London), University Professor and Head, Post-Graduate Department of History, Berhampur University, Orissa; Calcutta, 1981.