Lenné was born in Bonn, then part of the Electorate of Cologne, the son of the court and university gardener Peter Joseph Lenné the Elder (1756–1821), and his wife, Anna Catharina Potgieter (also Potgeter), daughter of the mayor of Rheinberg. The Lenné family descended from the Prince-Bishopric of Liège, Peter Joseph's ancestor Augustin Le Neu had settled in Poppelsdorf near Bonn as court gardener of Archbishop-Elector Maximilian Henry of Bavaria about 1665.
Having obtained his Abitur degree, Peter Joseph Lenné decided to adopt the family tradition. He began his apprenticeship as a gardener in 1808 with his uncle, Josef Clemens Weyhe, court gardener at the electoral Augustusburg and Falkenlust Palaces, Brühl. At the instigation of his father, he also took university courses in botany.
From 1809 to 1812, Lenné took many study trips, paid for by his father, which took him to Southern Germany, to France, and to Switzerland. In 1811, he completed a long internship in Paris with Gabriel Thouin, who was then one of the most famous garden architects in Europe. This made him a master landscaper. On another of these trips, Lenné made the acquaintance of the creator of the English Garden in Munich, the landscape gardener Friedrich Ludwig von Sckell, who would have a lasting influence on Lenné's work.
In 1812, Lenné followed his father to Koblenz, where he had been named Director of the Gardens by the Prefect Jules Doazan. Later in that year, Lenné became active at Schloss Schönbrunn, where he would remain until 1814. He then returned to Koblenz, where he was given private garden commissions until 1815. Extensions to the city's fortifications gave him an opportunity to propose a plan for its beautification by the addition of gardens; however, this was not carried out because of lack of funds. In 1816, he returned to Potsdam at the suggestion of Prussian forestry official Georg Ludwig Hartig and General Graf von Hacke. There he received the position of Assistant Gardener to the Court Garden Director at Sanssouci.
While still working as an assistant gardener, in spring 1816 Lenné received a commission from the Prussian Chancellor Karl August von Hardenberg to renovate the grounds around his country house at Klein-Glienicke. This work on Glienicke Palace, which would later become Prince Carl of Prussia's residence, laid the groundwork for Lenné's designs for the surrounding area of Potsdam, which he wanted to turn into a Gesamtkunstwerk. The upgrades of the Glienicke grounds were followed - in close cooperation with the architects Karl Friedrich Schinkel, Ludwig Persius, and Ferdinand von Arnim - by those of others such as the Böttcherberg and facing it Babelsberg Park, which was completed by Prince Hermann von Pückler-Muskau. Characteristic of Lenné's work are versatile sight axes - a horticultural stylistical device - which he applied at Sanssouci Park and elsewhere. As part of the Berlin-Potsdam cultural landscape, which stretches from the Pfaueninsel to Werder, many sites of Lenné's work are World Heritage Sites and have been under the protection of UNESCO collectively since 1990.