The oldest traces of human settlement in the Kostheim district date back to the Neolithic period. In Roman times, Kostheim was of strategic importance: initially as a military base for securing the crossing over the Main, then as a bridgehead for a fixed wooden bridge, which was built in the years 75-110 AD and crossed the river to the west of today's church. An army road from Kastel to Heddernheim also touched the village; the so-called Steinern Straße was part of it. Many finds indicate that a Roman settlement must have gradually developed in Kostheim. This era ended in 406 in a battle with the Alans, Suebi and Vandals. Kostheim has been of great importance as a river crossing since this time and it can be assumed that the Roman settlement site was taken over by the Germanic tribes. This is also indicated by the place name, which can be interpreted as early Frankish.

The next news of Kostheim is its first documentary mention in 790, when Charlemagne issued two documents in the "villa Copsistaino" on August 31 of that year. This name is derived from the Latin "caput stagni", "head on the marsh". Other forms of the name are "Chuffingstang", then "Cufstain" and since 1217 "C(h)ostheim". The patronage over the local church of St. Kilian as well as the tithes belonged to the Mainz nunnery of Altmünster, which was the most important landlord in Kostheim. This included the appointment and salary of the local priest and the bell ringer; the convent was also responsible for the upkeep of the church building. The Altmünster monastery also owned the ferry across the Main, which it leased to the Kostheim ferrymen in 1432; it had also leased its land in Kostheim to other ecclesiastical institutions. The lords of Eppstein probably also had their own manor in Kostheim. However, it is difficult to separate this from the bailiwick over Kostheim, which they received as a fief as early as the 12th century and had exercised by appointed sub-bailiffs. The central ecclesiastical authority was the archdeaconry of the provost of St. Peter in Mainz, Kastel deanery.

Blood jurisdiction over Kostheim was exercised by the Mechtildshausen district court, which belonged to the Kostheim district; the mayor and aldermen were responsible for civil jurisdiction and village administration. As has been documented since around 1330, the court met in or in front of the courtyard of the Lords of St. Stefan, in the courtyard of the Altmünster monastery or at the churchyard wall or in front of the cemetery. A mayor, Heinrich, is mentioned by name for the first time in 1281. The number of aldermen varied between three and 13. A court seal has been preserved from 1475. For a time, the court in Kostheim acted as a high court for Kelkheim, Münster, Heidesheim, Budenheim and Hattersheim (1517).

The Kostheim district extended to Ginsheim on the left bank of the Main and to Hochheim, Delkenheim, Erbenheim and Kastel on the right bank. Until 1528, Kostheim was one of the places with divided local and judicial rule: St. Stephan in Mainz held the local rule, the Lords of Eppstein as bailiffs held the judicial rule. When they sold Kostheim to the Landgraves of Hesse in 1492, among others, they retained the bailiwick until they sold it to the Archbishop of Mainz in August 1528. In the same year, the duties of the head and sub-head clerk, the beadle, the surveyor etc. were regulated in a Weistum. The duties of the parish priest of St. Kilian and his bell ringer, who was both organist and schoolmaster, were also described in detail. The school is first mentioned around 1500. Kostheim remained Catholic under the sovereignty of Mainz, even though the Reformation would have found its supporters in the village. Kostheim was burned down in 1552.

Kostheim also experienced hard times during the Thirty Years' War. The village was occupied by the Swedes, who founded Gustavsburg as a heavily fortified bastion on the left bank of the Main in the district belonging to Kostheim. The fields on the left bank of the Main and on the Maaraue were lost to Kostheim for good, the inhabitants had to perform forced labor and suffered under the burden of quartering. Kostheim continued to suffer from the consequences of the war for a long time; in 1673, the village had 113 properties, some of which were "desolate and empty". A total of 162 owners were counted.

Kostheim was already surrounded by a town wall in the Middle Ages, with an upper gate on Bruchstraße and a lower gate on the Main. The streets of Mathildenstraße, Margarethenstraße and Herrenstraße (where the lords of St. Stefan lived) are still reminiscent of the medieval buildings. The annually elected Letzmeisters were responsible for the security of the gates and walls.

In the 15th century, Kostheim was a wealthy village, as can be seen from a Salbuch in which the feudal dues are recorded. A barn on the corner of Herrenstrasse and Burgstrasse is a remnant of the tithe farm. Agriculture and viticulture flourished in the 18th century. In 1758, the school was singled out for special praise in school statistics. At the head of the administration in the 18th century were the head and sub-head bailiffs.

These peaceful and prosperous times came to an end with the Napoleonic Wars. When revolutionary France occupied Mainz in 1792 and the French faced each other in Kastel and the Germans in Hochheim, Kostheim became a battlefield. After being shelled several times, it was a field of rubble, and the parish church was also destroyed. In 1803 Kostheim, like Kastel, became part of the Nassau-Usingen district, and in 1806 it reverted to Mainz and became French. The boundary between Kostheim and Hochheim became the national border. After the Congress of Vienna, Kostheim and Kastel became part of the Grand Duchy of Hesse (Province of Rheinhessen, Canton of Mainz). In 1835 Kostheim became a town and in 1852 a district of Mainz. In 1806, the town had 1,024 inhabitants.

In 1808, at the request of Kostheim pastor Rößler, Napoleon granted Kostheim 25 years of tax exemption - a favor that prompted pastor Henrich to read a requiem for the deceased French emperor in 1821, contrary to the sovereign and ecclesiastical prohibition. In 1809, the so-called Neudörfche was built after a major fire. The village was rebuilt; by 1830, the "village" of Kostheim once again had 202 houses with 1,272 inhabitants, and in 1836 the new Kilianskirche church was consecrated.

The original economic structure of Kostheim was characterized by agriculture, fruit and wine growing, but a Kostheim skipper is mentioned as early as 1281, and in 1662 the fisherman Lorenz Rhein belonged to the Mainz fishermen's guild. A mill had existed since 1293 at the latest. Due to its convenient location at the confluence of the Main and Rhine and the bridge and ferry connections to the southern bank of the Main that have existed since early history, Kostheim has always been a transshipment point for goods and merchandise of all kinds. From the 16th century onwards, rafting developed into one of the main occupations of the people of Kostheim. In 1894, a state treaty stipulated the regulation of the Lower Main and the expansion of the Kostheim rafting port. Originally there were five sawmills in Kostheim, three of which had rafting rights. Kostheim's timber processing industry employed around 200 people until after the Second World War. Today, only the Peter Eider company still exists.

In the 1860s, MAN settled in Gustavsburg and developed into one of the leading bridge construction companies in Germany. The cellulose factory, which opened on June 1, 1885, became the most important employer. The Kostheim match factory (popularly known as the "Streichhölzer") was built in 1887 and employed around 100 people, mostly women. Production was discontinued at the end of 1930. In 1926, Lindes Eismaschinen AG founded a branch in Kostheim with 250 employees. In 1967, AEG acquired 75% of the shares in the Kostheim Linde plant. A major fire in 1971 destroyed the warehouse and production facilities. After reconstruction in 1989, production continued under the name Duofrost. In 2005, the plants were sold to Carrier GmbH and relocated to the Czech Republic.

The necessary modernization of the infrastructure began with the opening of the Taunusbahn railroad on the Wiesbaden-Frankfurt line in 1840. Kostheim lost the land required for the railroad construction without having its own railroad station. A fixed bridge over the Main was built in 1887/89. In 1907, Kostheim was connected to the Mainz streetcar network.

Partly as a result of the economic upturn, the population increased at the end of the 19th century from 2,971 in 1875 to 4,832 in 1895. Kostheim expanded westwards via Winterstraße around 1900 and as far as Am Mainzer Weg in 1916. Many street names are reminiscent of this time: Wilhelmstraße, Viktoriastraße, Louisenstraße, Ludwigstraße. The community received a girls' school in 1875 and the boys' school was extended in 1897. Numerous clubs were founded. In the 1870s, new buildings were erected on the other side of Winterstrasse and Berberichstrasse. Kostheim has had a Protestant congregation since this time, which was given its own church in 1906. Jewish residents, who have lived in Kostheim since around 1820, did not form their own community, but moved to Kastel. On 01.01.1913, Kostheim became part of the city of Mainz. However, the district of Gustavsburg was spun off in 1927. After the First World War, which brought the stationing of occupying troops to Kostheim, the "Siedlung Kostheim" district was created as a garden city with small terraced homes for 250 families. Kostheim developed into a village without a distinctive center and without a clear separation between factories and residential areas.

Industrial companies such as MAN, Cellulose and Linde were already geared towards the military requirements of war before 1936. MAN produced bridge parts and ship hulls, Cellulose basic materials for the production of ammunition, uniforms, aviation fuel and medical supplies. The Second World War left significant damage to the buildings of the settlement and Alt Kostheim. The street along Hochheimer Strasse was almost completely destroyed. The Catholic churches and today's parish center in the settlement were hit by bombs. 113 people were killed in air raids. After the Second World War, new residential areas such as the "Sampel" were built and new industries were established.

On 25.07.1945, Kostheim was incorporated into Wiesbaden. In 2003, there were still seven small farms with an area of less than two hectares. In addition, there were 13 full-time farms (mostly in viticulture, 66 ha), which cultivate a total of 191 ha of land. Today (as of 01.01.2016), 14,076 people live in 6,752 households in Kostheim.

A special feature is the annual pilgrimage of the parish of St. Kilian to Fischbach in the Taunus. According to statements that are not documented, the pilgrimage is said to have led to the miraculous image in the chapel of Gimbach as early as 1444. The reason was probably a great famine. Other sources speak of the time around 1666, a major plague year in which Kostheim was spared from the epidemic. In 1828, the pilgrimage was moved to the parish church in Fischbach at the insistence of the Duchy of Nassau government. Catholics from the parish still make an annual penitential pilgrimage there.

In 1751, two crossed vine knives were found engraved on a boundary stone from 1603. In the form of silver pincers on a red background, the image on the boundary stone was chosen as the coat of arms of Kostheim.