I have the same problem. My scenario was after getting the data inside SQLite Database file I want to delete that file but it always throw an error "...using by other process". Even I dispose the SqliteConnection or SqliteCommand the error still occur. I've fixed the error by calling GC.Collect().

Code snippet

public void DisposeSQLite()
{
    SQLiteConnection.Dispose();
    SQLiteCommand.Dispose();

    GC.Collect();
}

Hope this help.

In my case I was creating SQLiteCommand objects without explicitly disposing them.

var command = connection.CreateCommand();
command.CommandText = commandText;
value = command.ExecuteScalar();

I wrapped my command in a using statement and it fixed my issue.

static public class SqliteExtensions
{
    public static object ExecuteScalar(this SQLiteConnection connection, string commandText)
    {
        // Added using
        using (var command = connection.CreateCommand())
        {
            command.CommandText = commandText;
            return command.ExecuteScalar();
        }
    }
}

Then you can use it like this

connection.ExecuteScalar(commandText);

The following worked for me:  MySQLiteConnection.Close(); SQLite.SQLiteConnection.ClearAllPools()

I found edymtt's answer right about blaming TableAdapters / Datasets, but instead of modifying the every time re-generated TableAdapter codefile, I found an other solution: to manually call .Dispose on the TableAdapter's child elements. (In .NET 4.5, latest SQLite 1.0.86)

using (var db = new testDataSet())
{
    using (testDataSetTableAdapters.UsersTableAdapter t = new testDataSetTableAdapters.UsersTableAdapter())
    {
        t.Fill(db.Users);
        //One of the following two is enough
        t.Connection.Dispose(); //THIS OR
        t.Adapter.Dispose();    //THIS LINE MAKES THE DB FREE
    }
    Console.WriteLine((from x in db.Users select x.Username).Count());
}

In most cases the problem will arise if you don't dispose your readers and commands properly. There is a scenario in which commands and readers will not dispose properly.

Scenario 1: In case you are running a boolean function. before a result is reached the code in the finally block will not excecute. This is a big problem if you are going to be evaluating the results of function isDataExists while executing code if it suits the result i.e

    if(isDataExists){
        // execute some code
    }

The function being evaluated

    public bool isDataExists(string sql)
    {
        try
        {
            OpenConnection();
            SQLiteCommand cmd = new SQLiteCommand(sql, connection);
            reader = cmd.ExecuteReader();
            if (reader != null && reader.Read())
            {
                return true;
            }
            else
            {
                return false;
            }
        }
        catch (Exception expMsg)
        {
            //Exception
        }
        finally
        {
            if (reader != null)
            {
                reader.Dispose();
            }
            CloseConnection();
        }
        return true;
    }

Solution: Dispose your reader and command inside the try block as follows

            OpenConnection();
            SQLiteCommand cmd = new SQLiteCommand(sql, connection);
            reader = cmd.ExecuteReader();
            if (reader != null && reader.Read())
            {
                cmd.Dispose();
                CloseConnection();
                return true;
            }
            else
            {
                cmd.Dispose();
                CloseConnection();
                return false;
            }

Finally dispose the reader and command just in case some thing went wrong

        finally
        {
            if (reader != null)
            {
                reader.Dispose();
            }
            CloseConnection();
        }

As said earlier SQLite objects must be destroyed. However, there is a strange behavior: connection must be open during a call Dispose on commands. For example:

using(var connection = new SqliteConnection("source.db"))
{
    connection.Open();
    using(var command = connection.CreateCommand("select..."))
    {
        command.Execute...
    }
}

works fine, but:

using(var connection = new SqliteConnection("source.db"))
{
    connection.Open();
    using(var command = connection.CreateCommand("select..."))
    {
        command.Execute...
        connection.Close();
    }
}

gives the same file lock

This was one of the top google results I had found when I ran into this error. However, none of the responses helped me so after more searching around and googling I came up with this code that works from some of the code from http://www.tsjensen.com/blog/post/2012/11/10/SQLite-on-Visual-Studio-with-NuGet-and-Easy-Instructions.aspx

However, I did not have to use the NuGet at all. What my program does is downloads a db file from a server every time it is opened. Then if a user updates that db, it will be uploaded for everyone to get the next time they open the same program. I was getting the error that the file was in use after updating the local file and trying to upload it to our SharePoint. Now it works fine.

Public Function sqLiteGetDataTable(sql As String) As DataTable
    Dim dt As New DataTable()
    Using cnn = New SQLiteConnection(dbConnection)
        cnn.Open()
        Using cmd As SQLiteCommand = cnn.CreateCommand()
            cmd.CommandText = sql
            Using reader As System.Data.SQLite.SQLiteDataReader = cmd.ExecuteReader()
                dt.Load(reader)
                reader.Dispose()
            End Using
            cmd.Dispose()
        End Using
        If cnn.State <> System.Data.ConnectionState.Closed Then
            cnn.Close()
        End If
        cnn.Dispose()
    End Using
    Return dt
End Function

Ensuring that any IDisposable (e.g., SQLiteConnection, SQLiteCommand, etc) is properly disposed of solves this problem. I should re-iterate that one must be using "using" as a habit to ensure proper disposing of disposable resources.

I had the same problem and it was only fixed by disposing the DbCommand in the using statement, but with Pooling = true my problem was fixed!!

                SQLiteConnectionStringBuilder builder = new SQLiteConnectionStringBuilder
                {
                    Pooling = true
                };