R. Nathanson was the outstanding posek and writer of responsa of his generation. Problems reached him from all parts of the world and he corresponded with all the great contemporary scholars. In his works he is revealed principally as an instructor in practical halakhah. He regarded himself as responsible for the condition of halakhah in his time, in succession to such scholars as R. Akiva Eger and R. Moses Sofer. He was opposed to the method of pilpul for its own sake, regarding it as suitable only for youths (Divrei Sha'ul, Aggadot, 29b) but not for those destined to be religious teachers. He did not necessarily base his decision "upon the statements of aharonim" (Sho'el u-Meshiv, 2 pt. 3, no. 108), but based his rulings mainly upon the Talmud and the rishonim. He tended to leniency in his rulings, and took contemporary circumstances into consideration. He was one of those who permitted machine-baked mazzot in opposition to the view of R. Solomon Kluger. Although R. Kluger decided that etrogim from Corfu were invalid because of the fear that they were hybrids, R. Nathanson permitted them (Yosef Da'at, Kilei Begadim, no. 302). He also regarded the birds called "kibbitzer" hens as permitted according to the dietary laws although other authorities forbade them (Sho'el u-Meshiv, 3 pt. 2, no. 121). Although known for his permissive approach, however, he sometimes declared things forbidden simply as a precaution (Yosef Da'at, Terefot, 64–65). It was this which prompted R. Dov Berush Meisels, rabbi of Warsaw, to say of him: "I know him of old as one who adopts a stringent and not a lenient line" (end of the pamphlet Moda'ah le-Veit Yisrael). Despite his leniency in halakhic ruling, he fought with all his power against the progressives in his community who wanted to introduce reforms into education. When the government sought to compel the Jews of Galicia to send their children to government schools and to bar them from the heder until they had passed four classes of the secular schools, as well as to make the teachers pass an examination in German and pedagogy, R. Nathanson took the initiative in uniting the great talmudic scholars to obtain the repeal of the edict (see R. S. Kluger's letter of 1867 in Toledot Shelomo (1956), 113ff.).