The situation was changed by the granting of the de non tolerandis Judaeis privilege by King Sigismund August in 1556, as a result of which most of the Jews moved from Łomża to nearby Piątnica. With time, the policy towards Jews was relaxed and historical sources indicate that they settled in Łomża again in the second half of the 16th century. Shortly afterwards, in 1598, Jews were expelled from the town again (the privilege of King Sigismund III Vasa from that year allowed the Jews to stay in Łomża for no longer than three days). The reason for this was the economic crisis and the resulting intensified competition between Christian and Jewish merchants and craftsmen. At that time, Jews lived in Piątnica, as well as in Rybaki - a village at that time, which later became a Jewish district of Łomża.

The Jewish community in Łomża was re-established during the times of the Duchy of Warsaw. At that time, 157 Jews constituted slightly more than 10% of all the inhabitants of Łomża (data from 1808). At the beginning of its existence, the community of Łomża used the services of the rabbi from Śniadowo and the local cemetery. The Jewish cemetery in Łomża was opened in the first half of the 19th century. During the period of the Kingdom of Poland, despite the efforts of the central authorities to separate Jewish districts in larger towns, the Jews of Łomża were allowed to settle in the whole town. In 1827, 948 Jews lived in the town (29% of the town's population), thirty years later - 2608 (44.3%). In the first half of the 19th century Jews played an important role in the economic life of the town. They were mainly engaged in trade. The richest merchants focused on colonial, foreign, ell-measured or Nuremberg goods (haberdashery, combs, pins, etc.), others also traded food products, salt, fish, iron, leather and glassware. The Łomża Jews were also engaged in craft - they were tailors, shoemakers, bakers, butchers, hatters, tinsmiths and glass makers.

Many eminent rabbis were connected with Łomża, including: Beniamin Diskin, Eliahu Chaim Maisel, Elizer Symcha Rabinowicz. In 1880 a great synagogue was built in the town, where a yeshiva operated. There was also a second synagogue in the suburbs. At the end of the 19th century, Jews were employed in large numbers in industrial plants operating in the town, where they constituted more than half of all workers. In 1893, 8767 Jews lived in Łomża, which constituted 47.8% of Łomża's population, whereas in 1931 there were 8912 Jews (35.6% of the town's population).

After the outbreak of World War II, in September 1939, during the fights between Polish and German armies, Łomża suffered greatly. As a result of the bombing, the great synagogue was also destroyed. From 28 September 1939 the town was in the Soviet occupation zone. The Germans entered Łomża again in June 1941, and in August they established a ghetto, moving all the Jews of Łomża, about 10 thousand people, to it. Between June and September the occupiers killed about 3800 Jews, of which about 2200 were shot in the forests near Giełczyn. On 1 November 1942, due to the liquidation of the ghetto, about 8,000 Łomża Jews were moved to the transit camp in Zambrów, from where most of them, in January 1943, were sent to the Auschwitz-Birkenau death camp.

The Jewish cemetery in Boczna Street was established around 12 February 1882, due to the lack of space for new burials in the existing cemetery, located in Rybaki Street. The ancestors of the President of Israel Chaim Herzog were buried in the necropolis. During World War II, scouts, some of whom were of Jewish origin, were shot in the cemetery. In the 1960s the site of execution was commemorated by a four-metre cross surrounded by a wooden railing. The exact location of the grave is currently unknown. The cemetery was open until the Holocaust.

After World War II the necropolis fell into ruin. In the late 1960s, the Łomża Jewish Cemetery Foundation started cleaning up the cemetery, and an inventory of tombstones was initiated, which is still being worked on.

The cemetery is located in the eastern part of Łomża, behind the buildings along Wąska and Boczna streets. Currently it occupies a rectangular plot of about 80 x 240 m (about 1.9 ha), located on a gentle slope. On the main axis of the cemetery, on Wąska Street, there is a former pre-burial house (now a residential building). Next to it, there was probably the main gate, which has not been preserved. Currently, the entrance to the cemetery is located at the junction of Boczna and Górna streets. The area is fenced, the historical wall is preserved on the west side.

It is estimated that there are about 4 thousand graves in the cemetery, with over 600 tombstones remaining. The largest concentration of tombstones is located in the south-western part of the necropolis, while the most destroyed part is in the vicinity of Górna Street. The division into quarters for men and women is still clear. The tombstones are arranged in rows, made of sandstone and marble. They range from traditional matzevot to tombstones in the form of columns and obelisks. Inscriptions were made in both Hebrew and Polish. The appearance of tombstones illustrates not only the development of sepulchral art, but also the process of assimilation of Łomża Jews.

At the main avenue of the cemetery there is a white brick ohel of Rabbi Malkiel Tennenboim. It is now devoid of the original epitaphic plates. The inscription engraved on the basis of the tombstone of Cwi Hirsz Truskier who died in 1906 is a trace of the tragic fate of the Jews of Łomża: “Site of execution of the Jewish population, murdered by the Nazis in 1941–1945”.