He was born at Ditcheat, Somerset, where his father was rector. He was a younger brother of William Alleine, the saintly vicar of Blandford. Richard was educated at St Alban Hall, Oxford, where he was entered commoner in 1627, and whence, having taken the degree of B.A., he transferred himself to New Inn, continuing there until he proceeded M.A. On being ordained he became assistant to his father, and immediately stirred the entire county by his burning eloquence.
In March 1641 he succeeded the many-sided Richard Bernard as rector of Batcombe, Somerset. He declared himself on the side of the Puritans by subscribing "The testimony of the ministers in Somersetshire to the truth of Jesus Christ" and the Solemn League and Covenant, and assisted the commissioners of the parliament in their work of ejecting unsatisfactory ministers. Alleine continued for twenty years rector of Batcombe and was one of the two thousand ministers ejected in 1662. The Five Mile Act drove him to Frome Selwood, and in that neighborhood he preached until his death in 1681.
His works are all of a deeply spiritual character. His Vindiciae Pietatis (which first appeared in 1660) was refused license by Archbishop Sheldon, and was published, in common with other nonconformist books, without it. It was rapidly bought up and "did much to mend this bad world." Roger Norton, the king's printer, caused a large part of the first impression to be seized on the ground of its not being licensed and to be sent to the royal kitchen. Glancing over its pages, however, it seemed to him a sin that a book so holy and so salable should be destroyed. He therefore bought back the sheets, says the historian Edmund Calamy, for an old song, bound them and sold them in his own shop. This in turn was complained of, and he had to beg pardon on his knees before the council-table; and the remaining copies were sentenced to be " bisked," or rubbed over with an inky brush, and sent back to the kitchen for lighting fires. Such "bisked" copies occasionally occur still. The book was not killed. It was often reissued with additions, The Godly Man's Portion in 1663, Heaven Opened in 1666, The World Conquered in 1668. He also published a book of sermons. John Wesley credited him as the originator of the covenant prayer that he introduced into Methodism in 1755.