The Temple was always meant to be a place of prayer, as we see from Solomon's dedication speech for the first Temple (Kings I Ch. 8):
[Therefore] turn to the prayer of Your servant, and to his plea, Adonoy, my God; to listen to the song and to the prayer that Your servant prays before You this day:
29That Your eyes be open toward this Beis Hamikdosh night and day, to the place of which You said, ‘My Name will be there; to listen to the prayer that Your servant will pray at this place.
30And listen to the plea of Your servant, and of Your people, Yisroel, that they will pray toward this place; and You will listen in the place of Your dwelling, in the heavens, and You will listen and forgive.
31Should a person sin against his fellow man, and is liable that a curse be upon him, and the curse comes before Your Altar, in this House;
32May You listen from the heavens, and act and judge Your servants, to condemn the wicked one, to set his [evil] way upon his head; and to justify the righteous one, to give him according to his righteousness.
33When Your people, Yisroel are defeated by an enemy because they sinned against You; and they turn to You and praise Your Name, and pray and beseech You in this Beis Hamikdosh.
34May You listen from the heavens, and forgive the sin of Your people, Yisroel; and return them to the land that You gave to their fathers.
35When the heavens are closed off and there is no rain, because they sinned against You; and they pray toward this place and praise Your Name, and repent of their sins, for You to answer them.
36May You listen from the heavenss and forgive the sin of Your servants and Your people, Yisroel, for You will teach them the right way so they will walk in it; and give rain on Your land that You gave to Your people for an inheritance.
37Should there be a famine in the land, or should there be a plague, or if the crops be endangered by wind or rot, locusts or similar insects; or if their enemy besiege them within the land, at the gates of their cities, or any affliction or sickness.
38Every prayer, every plea that any person will make, [or] by Your people, Yisroel, since every person knows the affliction of his heart; and he will spread out his hands to this Beis Hamikdosh.
39May You listen from the heavens, Your Dwelling Place, and forgive and act, and give to each one according to all his ways, for You know his heart; for You alone know the hearts of all the children of men.
40That they may fear You all the days that they live on the face of the earth, that You gave to our fathers.
41And even to the stranger who is not of Your people Yisroel, and comes from a far off land for the sake of Your Name.
42For they will hear about Your great name, and of Your mighty hand and of Your outstretched arm, and they will come to this House and pray.
43May You listen from the heavens, Your dwelling place, and do according to all that the stronger calls out to You; so that all the people of the land will know Your Name, to fear You as do Your people, Yisroel, and they will know that your name is called upon this Beis Hamikdosh, that I have built.
44When your people go out to war against their enemy, in the manner that you send them, and they will pray to Adonoy by way of the city that You chose, and the house that I built for Your Name.
45May You listen from the heavens to their prayers and their pleas, and render their judgement.
The three daily prayers were instituted by the Sages to correspond to the sacrifices, but there always was a biblical commandment to pray, either once daily (according to Maimonides) or in times of trouble (Nachmanides).
