Fundamentally Amyraut took issue with contemporary Calvinists who shaped their system of theology around the decree of predestination. The entire body of divinity in much of seventeenth century Reformed theology was subsumed under the doctrines of sovereign election and reprobation. Amyraut insisted that the chief doctrine of Christian theology is not predestination but the faith which justifies. Commitment to justification by faith as the overarching theme denoted a theology as truly reformational. Moreover, Amyraut rightly argued that Calvin discussed predestination not under the doctrine of God but following the mediation of salvation blessings by the Holy Spirit. For Amyraut predestination is an inscrutable mystery, which offers an explanation of the fact that some accept Christ whereas others reject him.
Amyraut also developed a system of covenant theology alternative to the twofold covenant of works, covenant of grace schema propounded by much of Reformed orthodoxy. The Saumur school postulated a threefold covenant, viewed as three successive steps in God's saving program unfolded in history. First, the covenant of nature established between God and Adam involved obedience to the divine law disclosed in the natural order. Second, the covenant of law between God and Israel focused on adherence to the written law of Moses. And finally the covenant of grace established between God and all mankind requires faith in the finished work of Christ. In Amyraldianism the covenant of grace was further divided into two parts: a conditional covenant of particular grace. For actualization the former required fulfillment of the condition of faith. The latter, grounded in God's good pleasure, does not call for the condition of faith; rather it creates faith in the elect.
Amyraut's covenant theology, particularly his division of the covenant of grace into a universal conditional covenant and particularly undiconditional covenant, provided the basis for the unique feature of Amyraldianism, namely, the doctrine of hypothetical universal predestination. According to Amyraut there exists a twofold will of God in predestination, a universal and conditional will, and a particular and unconditional will. Concerning the first, Amyraut taught that God wills the salvation of all people on the condition that they believe. This universal, conditional will of God is revealed dimly in nature but clearly in the gospel of Christ. Implicit in this first will is the claim that if a person does not believe, God has not, in fact, willed his or her salvation. Without the accomplishment of the condition (i.e., faith) the salvation procured by Christ is of no avail. Amyraut based his doctrine of hypothetical universal predestination on such biblical texts as Ezek. 18:23; John 3:16; and 2 Pet. 3:9.
Rather he must preach Christ as the Savior of the world and call for faith in his sufficient work. Only the universal, conditional will of God is the legitimate object of religious contemplation. Amyraldianism thus involves a purely ideal universalism together with a real particularism.
The issue of the intent or extent of Christ's atonement is implicit in the foregoing discussion. Amyraldianism postulated a universalist design in the atonement and a particular application of its benefits. The salvation wrought by Christ was destined for all persons equally. Christ legitimately died for all. Nevertheless only the elect actually come into the enjoyment of salvation blessings. Amyraldianism thus upheld the formula: "Jesus Christ died for all men sufficiently, but only for the elect efficiently."
Amyraut believed that his teachings on the twofold will of God and twofold intent of the atonement were derived from Calvin himself. He viewed his theology as a corrective to much of seventeenth century Calvinism, which denied the universal, conditional will of God in its preoccupation with the unconditional decree. And he disputed with Arminianism, which failed to see that a person's salvation was effectively grounded in the absolute purpose of God conceived on the basis of his own sovereign pleasure. And finally Amyraldianism provided a rapprochement with Lutheranism and its interest in justification by faith and the universality of Christ's atoning work. Some later Reformed theologians such as Charles Hodge, W G T Shedd, and B B Warfield insisted that Amyraldianism was an inconsistent synthesis of Arminianism and Calvinism. Others, however, such as H Heppe, R Baxter, S Hopkins, A H Strong, and L S Chafer maintained that it represents a return to the true spirit of Holy Scripture.