From the autumn of 1605 until 1609, Christoph Scheiner studied theology in Ingolstadt. Due to his invention of the pantograph, he had already gained celebrity status. Duke William V of Bavaria even invited him to Munich to demonstrate the instrument.

On March 14, 1609, he entered Holy Orders as a Deacon. He was ordained by suffragan bishop Marcus Lyresius. Scheiner finished his studies on June 30, 1609 with his first work, ‘’Theses Theologicae’’ and with a disputation (PhD in theology). On April 18, 1609, he received his major orders from suffragan bishop Marcus Lyresius in Eichstätt, from where he went to Ebersberg to serve his tertianship with Father Johannes Pelecius SJ. In the years between 1610 and 1616/1617, Scheiner worked as a successor to Father Johannes Lantz SJ in Ingolstadt, teaching mathematics (physics and astronomy) and Hebrew. He lectured on sun dials, practical geometry, astronomy, optics and the telescope.

In 1611, Scheiner observed sunspots; in 1612 he published the "Apelles letters" in Augsburg. Marcus Welser had the first three Apelles letters printed in Augsburg on January 5, 1612. They provided one of many reasons for the subsequent unpleasant argument between Scheiner and Galileo Galilei. Scheiner published in 1614 the Disquisitiones mathematicae in Ingolstadt with Johann Georg Locher, in 1615 Sol ellipticus in Augsburg and with Georg Schönberger Exegesesfundamentorum gnomonicorum in Ingolstadt, and in 1617 he published Refractiones coelestes, also in Ingolstadt. Cristoph Scheiner took his remaining vows of poverty, chastity, obedience and loyalty before the Pope on July 31, 1617 in the town of Ingolstadt under Father Johannes Manhart SJ. In the very same year Scheiner made known his wish to go to China as a missionary. Father General Mutio Vitelleschi sent him a letter, however, telling Scheiner he had better stay in Europe and persevere with his mathematical studies. In the winter of 1617 - 1618, Scheiner returned to Innsbruck, Austria at the behest of Archduke Maximilian III.

After November 1614, Archduke Maximilian III summoned Christopher Scheiner to Innsbruck several times to discuss astronomical and mathematical questions. The Archduke had received an astronomical telescope with two convex lenses which showed objects upside down and the wrong way round. Scheiner added a third lens, thus manufacturing a terrestrial telescope which allowed Maximilian to see the beautiful stretches of his country while standing upright. A portable camera obscura was developed by Christoph Scheiner in Innsbruck. Furthermore a walkable camera obscura was constructed.

After the death of Maximilian III in 1618, Archduke Leopold V was appointed imperial representative of Tyrol and of the Upper Provinces. Like his predecessor Maximilian, Leopold V put his trust in Father Scheiner. Scheiner’s "Oculus hoc est: Fundamentum opticum," containing many new insights into the physiological nature of the eye, was published in Innsbruck in 1619. The book had been written earlier in Ingolstadt. Oculus is subdivided into three parts: the first part treats the anatomy of the eye, the second part the refraction of the light ray inside the eye, and the third part deals with the retina and the visual angle. Scheiner once again chooses the way of observation and experiment. Like Kepler before him, he found that the retina is the seat of vision and that the optic nerve transmits the images from the retina to the brain. Scheiner was rebuked once more for going from Innsbruck to Hall in a heavily loaded coach drawn by six horses! Father General Vitelleschi wrote him a letter. Archduke Leopold V and Father Scheiner carried on a sizeable correspondence from 1620 until 1632. One of Scheiner’s letters to Leopold from 1626 informs the Archduke that Galilei is not to hear of Scheiner’s work concerning the sunspots.

The inventory of Leopold’s library contains works by Tycho Brahe and Galileo Galilei: Leopold lead a friendly correspondence with Galilei. On May 23, 1618, Leopold received telescopes from Galilei, along with a treatise on the sunspots, the Discorso del Flusso e Reflusso del Mare.

Christopher Scheiner was the builder of the new Jesuit church in Innsbruck. Craftsmen began to work on the roof in the July 1624, but September saw a sudden collapse of the middle part of the gallery and the sidewall facing the street. According to a new decision, the church had to be turned by 90° and be reconstructed.

Freiburg University was facing a decline at the beginning of the 17th century. It was on November 16, 1620, that Archduke Leopold summoned the Jesuit Fathers, first of all, the "most excellent by far" Christopher Scheiner. In the spring of 1621, Scheiner was recalled for reasons confirmed to be unknown: in fact it was Archduke Karl's wish to have Scheiner as his father confessor. Archduke Karl had travelled with Scheiner from Brixen to Vienna, from where he did not return to Neisse until sometime between 1621 and 1622. In February 1623, Scheiner was appointed Superior of the future college. Then the Spanish King Philipp IV chose Karl of Austria for the office of a vice king of Portugal. Archduke Karl travelled to Madrid. Scheiner had to travel to Rome, to instigate the foundation of the new college in Neisse. Scheiner stayed in Rome longer than his duty required. In Rosa Ursina sive Sol, he wrote that he had been sent to Rome "ad summum pontificem, ob certa peragenda negotia" (Latin meaning "to the pontifical summons..."). Other theories, contending that Scheiner had been summoned to Rome as an expert astronomer because of Galilei, or that he felt his transfer to Neise was a punishment, have not been confirmed. It was only 13 years later, that he returned to Neisse via Vienna, where he stayed for some time.

When Scheiner went to Rome in 1624, friends asked him to write about his solar observations. At last he had time for mathematical books, among them Galilei’s Il saggiatore, which contains plagiarisms of Scheiner’s work while accusing the Jesuit of plagiarizing himself. In 1629 and 1630, Scheiner observed Mock suns (parhelia) and halos; his observations also included an eclipse on April 8, 1633. On June 22, 1633, Galilei received his sentence and had to renounce his claims, despite the protest sounding even from the Catholic side. Scheiner’s influence on the trial cannot be proven. The trial files merely contain a small note mentioning that he had opposed the Copernicans. At the time of the trial, Scheiner was still in Rome, staying at the seminary for future priests. Scheiner wrote three of his books in Rome: Rosa Ursina sive Sol (Bracciano, 1626 – 1630), on the sunspots which served as a standard work for research work on the sunspots for a long time. Rosa Ursina sive Sol contains four books. In the first part, Scheiner discusses the question of priority of discovery in regard to the sunspots. The second part not only describes telescopes, different kinds of projection and the helioscope but also compares the optics of the telescope to the physiological optics of the eye. In the third book, Scheiner presents a comprehensive collection of the data from his observation of the sunspots. Book 4 consists of two parts: The first part deals once again with solar phenomena like sunspots and sun flares, the sun’s rotation period of 27 days and the inclination of its axis of rotation. In the second part, Scheiner mentions numerous passages and quotations from the Bible, the writings of the Church Fathers and philosophers to prove that his geocentric view is in accordance with the teachings of the Catholic Church. Scheiner published Pantographice, about the pantograph which he had invented as early as 1603, and finally in 1632 - 1633, Scheiner published his last work Prodromus, a pamphlet against the heliocentric theory which was published posthumously in 1651.

Father General Mutio Vitelleschi wrote his first letter to Scheiner in Vienna on January 21, 1634. Thus Scheiner must have returned to Vienna between December 1633 and January 1634. Scheiner was unwilling to go back to Neisse. In Vienna, Scheiner was forced to confront the insecure funding for his book Rosa Ursina sive Sol.

After November 15, 1637, Scheiner was in Neisse. Scheiner’s activities in Neisse: Advisor, Councilor of the Rector, Mentor and Father Confessor to the students. Scheiner’s obituary from 1650 maintains that Scheiner had to stay in Vienna because of the war, that he had had to flee from Neisse with all his astronomical instruments, that he usually got up early, to write or read, take care of the garden and plant trees with his own hands. The author of this obituary mentions Scheiner’s modesty and chastity while pointing out that he was envied by many and "struggled with envy himself." Christoph Scheiner died on July 18, 1650 in Neisse (now Nysa, Poland).

The primary school in Markt Wald is named in memory of Christopher Scheiner. In Markt Wald, there is also a street and a plaque hangs on the town hall and an observation tower to his remembrance. In Ingolstadt, there is the Christoph - Scheiner - Gymnasium (a High School). The street to the observatory of the university in Munich and a road in Berlin (Charlottenburg) are named after Scheiner. In 1999, a coin (35-mm diameter), with Scheiner’s face on it, was minted in Ingolstadt. Also a lunar crater is named after Christopher Scheiner. A postage stamp was issued in Austria (2005). The town museum in Ingolstadt shows an oil painting (after 1732), also the Studienbibliothek Dillingen a fresco (painter Ignaz Schilling, 1702 – 1773).