Saroj Poddar-led Zuari Group had launched an open offer on April 20 to buy additional 4.33 crore shares, representing 36.56 per cent stake in MCFL, at Rs 91.92 per share.
Prior to the open offer, the group had 16.47 per cent stake in MCFL.
The acquisition of controlling stake also marks the end of the takeover battle between Zuari Group and Pune-based Deepak Fertilisers.
Zuari was competing with Deepak Fertilisers for taking control of MCFL since July 2013, but the latter withdrew from the race and has been selling shares of MCFL via open market since December 2014.
In a filing to the BSE, Zuari Agro Chemicals Ltd (ZACL) said, "Zuari Fertilisers and Chemicals Ltd (ZFCL), a wholly owned subsidiary of the company has acquired additional 36.56 per cent (totalling 53.03 per cent) equity shares of MCFL and therefore MCFL has become a subsidiary of ZFCL."
Consequently, MCFL has also become subsidiary of ZACL.
Meanwhile, Zuari Group has pledged its 16.47 per cent stake in MCFL to HDFC and IL&FS to partly finance its nearly Rs 400 crore open offer.
In its open offer, Zuari Group got a good response from MCFL shareholders as 5.2 crore shares were tendered against the offer of 4,33,29,000 shares.
"Our open offer has been oversubscribed and I am planning to meet Vijay Mallya by the end of this month. I along with Mr Mallya, will work towards making MCFL one of the premier fertiliser companies in the country," Zuari Group chief Saroj Poddar had said earlier this week.
UB Group, the original promoter, has 21.97 per cent stake.
As per the shareholding pattern on the BSE, both Zuari Group and UB Group are in the list of promoters.
Together, they will have 75 per cent stake in MCFL.
Zuari Group had announced the open offer in December 2014 to buy 4,33,29,000 shares in MCFL at Rs 91.92 per share.
Meanwhile, Pune-based Deepak Fertilisers has reduced its stake in the MCFL to 6.43 per cent from 31.25 per cent in December last year.
MCFL has a urea plant near Mangalore port with an annual capacity to produce about 4 lakh tonnes of urea and about 3 lakh tonnes of phosphatic fertilisers.
Zuari Group has a fertiliser plant in Goa.