I'm assuming that you'll only be using this new property for the purpose of your manufacturing business (e.g. you're not planning on letting any of it to a tenant), and all of your businesses income is subject to VAT?
If so - then subject to the normal VAT recovery requirements (holding proper VAT invoices, etc.) you will be able to recover the full amount of the VAT charged on your quarterly VAT return. This might mean that the quarter will show an amount payable to you (i.e. the VAT you can reclaim on your expenditure exceeds the VAT you're required to pay over on your income) - if so, HMRC will pay the difference to you.
You may find that the significance of the figure on the VAT return is such that it gets flagged by HMRC's systems for a check. It should be easy to demonstrate that it's a valid claim, but if you're due a repayment from HMRC for the return, this process may delay repayment. There is an automatic process where if HMRC make a late repayment, an amount of interest is calculated and added on. Obviously you'll still have the cashflow issue of having to pay the seller before being able to reclaim the VAT from HMRC.
Capital Goods Scheme
At the start, I checked that your business only generated taxable business (i.e. "vatable") income. That was because businesses generating only VAT-exempt income aren't normally entitled to recover the VAT they incur on their expenditure. Businesses that have a mixture of taxable and exempt income must undertake an apportionment known as "partial exemption".
Were it not for the Capital Goods Scheme, a business whose income was normally VAT-exempt could buy the building, briefly put it to taxable use in order to recover the VAT incurred on purchase, before then putting it to their normal VAT-exempt use. The Capital Goods Scheme prevents this by requiring you to consider the use over a ten-year period. VAT can still be reclaimed in full on purchase if the initial use is taxable business. But if at any point over the first ten years the use changes to VAT-exempt, a proportion of the VAT claimed on purchase must be returned to HMRC. The records that you're required to retain under HMRC's guidance are those which you would need to be able to calculate the VAT repayable to HMRC if your use of the building changed.
Given the significance of this transaction, you may want to seek advice, from your accountant or a VAT advisor - who will have a more detailed knowledge of your business. There are other considerations, including what you should do if you want to let any part of the building to someone else, or sell the building (or entire business) at a later stage. But I hope this gives you some comfort that (apart from the cashflow issue of having to wait for your quarterly VAT return to get the refund), the VAT on the purchase shouldn't be a cost to you.